UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 14A

(Rule 14A-101)

PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE

SECURITIES EXCHANGE ACT OF 1934

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Athira Pharma, Inc.

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Maximizing Long-Term Value for All Shareholders April 2022 A D VA N C I N G N E W TH E R A P I E S FOR N E U R ON A L H E A LTH

Disclaimer This presentation contains “forward-looking statements” within the meaning of Section 27A of the Securities Act of 1933, Section 21E of the Securities Exchange Act of 1934 and the Private Securities Litigation Reform Act of 1995. These forward-looking statements are not based on historical fact and include statements regarding fosgonimeton as a potential treatment for Alzheimer’s disease, Parkinson’s disease dementia, Dementia with Lewy bodies, and other dementias; Athira’s platform technology and potential therapies; future development plans; clinical and regulatory objectives and the timing thereof, including the timing of the ACT-AD and LIFT-AD clinical trials and the timing of the Phase 2 clinical trial of fosgonimeton for treatment of Parkinson’s disease dementia; interactions with regulators and the timing thereof, including anticipated timing of IND or equivalent submissions; expectations regarding the potential efficacy and commercial potential of Athira’s product candidates; the anticipated reporting of data; and Athira’s ability to advance its product candidates into later stages of development. Forward-looking statements generally include statements that are predictive in nature and depend upon or refer to future events or conditions, and include words such as “may,” “will,” “should,” “on track,” “would,” “expect,” “plan,” “believe,” “intend,” “pursue,” “continue,” and other similar expressions, among others. Any forward-looking statements are based on management’s current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements. These risks and uncertainties include, but are not limited to, the impact of a contested election at Athira’s annual meeting; the preliminary data for Athira’s fosgonimeton product candidate from the Phase 1a/b trials will not continue or persist in current or planned clinical trials; cessation or delay of any of the ongoing clinical trials and/or Athira’s development of fosgonimeton and other product candidates may occur; future potential regulatory milestones of fosgonimeton and other product candidates, including those related to current and planned clinical studies may be insufficient to support regulatory submissions or approval; the impact of the COVID-19 pandemic on Athira’s business, research and clinical development plans and timelines and results of operations, including impact on Athira’s clinical trial sites and contractors who act for or on Athira’s behalf, may be more severe and more prolonged than currently anticipated; the regulatory process for Athira product candidates; the outcome of legal proceedings that have been or may in the future be instituted against us and certain of our directors and officers; clinical trials may not demonstrate safety and efficacy of any of Athira’s product candidates; Athira’s assumptions regarding the sufficiency of its cash, cash equivalents and investments to fund its planned operations may be incorrect; Athira’s research and development efforts and its ability to advance product candidates into later stages of development may fail; any one or more of Athira’s product candidates may not be successfully developed, approved or commercialized; adverse conditions in the general domestic and global economic markets; the impact of competition; while P300 latency is a functional measure that is highly correlated with cognition, Athira may not successfully establish a connection between these P300 latency results and improved cognition; regulatory agencies may be delayed in reviewing, commenting on or approving any of Athira’s clinical development plans as a result of the COVID-19 pandemic, which could further delay development timelines; the impact of competition; the impact of expanded product development and clinical activities on operating expenses; the impact of new or changing laws and regulations; as well as the other risks detailed in Athira’s filings with the Securities and Exchange Commission. These forward-looking statements speak only as of the date hereof and Athira undertakes no obligation to update forward-looking statements. Athira may not actually achieve the plans, intentions, or expectations disclosed in its forward-looking statements, and you should not place undue reliance on the forward-looking statements. © Athira Pharma, Inc. All Rights Reserved. 2    

Table of Contents Executive Summary 4 An Introduction to Athira 6 Achieving Target Milestones and Executing with Strength for the Future 16 Highly Qualified Board with Experience Athira Needs for Pivotal Chapter 27 Kayne’s Campaign Not in the Best Interest of All Shareholders 32 © Athira Pharma, Inc. All Rights Reserved. 3    

Executive Summary

Executive Summary • Poised to report topline results from Phase 2 ACT-AD study by end of 2Q22 Successfully executing • Expect to complete enrollment for expanded LIFT-AD Phase 3 study by 3Q22, with larger sample size enhancing potential for single pivotal clinical study strategic drug development • Dosed first patient in SHAPE Phase 2 clinical trial of fosgonimeton in Parkinson’s disease dementia and Dementia with Lewy bodies in January 2022; priorities for Alzheimer’s positive results from this proof-of-concept trial would strengthen the potential pan dementia utility of fosgonimeton and increase confidence in the mode of Disease and other dementias action with large patient populations • Launched Phase 1 clinical trial for ATH-1020 that have significant unmet • Successful execution reflected in stock price performance – from the day of public announcement that Dr. Kawas resigned and Dr. Litton was appointed CEO need and market potential (October 21, 2021) through the day that Athira filed its preliminary proxy statement publicly disclosing Mr. Kayne’s director nominations (March 25, 2022), our stock price increased by ~32%, while the SPDR S&P Biotech ETF (XBI) index decreased by ~28% over the same period • CEO Mark Litton, PhD, MBA has 25+ years experience in the biopharma industry, including C-suite roles at 3 publicly traded companies — Previously served as President and COO of Alpine Immune Sciences. Prior to Alpine, spent 14 years at Alder Biopharmaceuticals, where he was co-Strong management team led founder and Chief Business Officer directly responsible for raising ~$1B in equity capital and led negotiations for numerous corporate alliances with by CEO Mark Litton with deep biotech and pharmaceutical companies prior to its sale to Lundbeck for ~$2B industry, R&D and • COO Rachel Lenington, MBA has 20+ years of strategic and operational leadership experience in drug development, commercialization and launch commercialization expertise to drive future shareholder value • Chief Medical Officer Hans Moebius, MD, PhD, ECPM, FAAN is an internationally recognized expert in neuropsychiatry, with 30+ years of experience in drug R&D and regulatory strategy, and has led several CNS projects to successful approval, including Namenda, the second leading AD therapy worldwide • CFO Glenna Mileson has 25+ years of financial and business management experience at biopharmaceutical and other companies The right board with diverse and • Highly qualified, experienced board with the right skills for Athira: clinical development, regulatory approval, commercialization, finance & financial planning, curated skillsets to oversee capital allocation, BD, legal & risk management and investment management Athira’s growth during pivotal • Record of systematically and thoughtfully adding experience and expertise, including 2 new independent directors YTD in 2022 and 3 in the past year chapter Mr. Kayne’s self-serving • Mr. Kayne has rebuffed multiple attempts by our board to constructively engage in order to avoid a costly, unnecessary proxy contest campaign is misguided and • Mr. Kayne has pushed an agenda to appoint himself to the board and terminate our CEO, and also have us resume a relationship with our former CEO, Dr. detrimental to the interests of Kawas all shareholders • Messrs. Kayne and Bickerstaff are generalists; they do not add to the skills that are already well represented on the board This proxy contest is a needless distraction at a time when Athira should be focused on delivering the results of the Phase 2 ACT-AD study © Athira Pharma, Inc. All Rights Reserved. 5    

An Introduction to Athira

OUR MISSION To restore lives by advancing bold therapies for neuronal health, thoughtfully and urgently

Company Overview • We are a late clinical-stage biopharmaceutical company developing small molecules to advance new therapies for a broad range of neurological diseases with significant unmet need Expected Key • We have a deep understanding of the multifactorial and complex pathologies associated with Near Term neurodegeneration Catalysts • We are familiar with the regulatory approval process for the treatment of Alzheimer’s disease (AD), and know what it takes to earn approval and for successful commercialization • Our lead program, fosgonimeton (ATH-1017), is based on strong science using a novel approach Topline data by to leverage a naturally occurring repair mechanism end of 2Q22 • Large patient populations with significant unmet need and market potential: • Compelling data in mild-to-moderate Alzheimer’s patients suggesting improved neuronal connectivity Enrollment complete LPI 3Q22 • Opportunities to expand into additional indications including Parkinson’s Disease Dementia Topline data 1H23 (PDD) and Dementia with Lewy Bodies (DLB) • Founded in 2011 and headquartered in Bothell, WA © Athira Pharma, Inc. All Rights Reserved. 8    

Athira Has Significantly Outperformed the Biotech Index and Neurodegeneration Peers Since Dr. Litton Was Appointed CEO Since IPO Last One-Year Since Dr. Litton Appointed CEO 160% 100% 80% 140% 80% 60% 120% 60% 100% 40% 32.3% 80% 40% 20% 60% 20% 40% 0% 20% 0% 11.0% 0% (20%) (20%) (27.1%) (27.6%) (22.7%) (29.6%) (20%) (25.1%) (32.6%) (40%) (40%) (40.9%) (40%) (60%) (60%) (60%) Sep-2020 Mar-2021 Sep-2021 Mar-2022 Mar-2021 Jul-2021 Nov-2021 Mar-2022 Oct-2021 Dec-2021 Jan-2022 Mar-2022 Athira Pharma SPDR S&P Biotech ETF (XBI) Neurodegeneration Peers Source: Market data as of 25-Mar-2022, the day that Athira filed its preliminary proxy statement publicly disclosing Mr. Kayne’s director nominations. Note: Charts reflect total shareholder return. Athira’s IPO occurred on 18-Sep-2020 and chart reflects the return relative to its IPO price of $17 per share. Dr. Litton’s appointment was publicly announced on 21-Oct-2021. Neurodegeneration Peers reflects average performance among AC Immune, Alector, Biogen, Cortexyme, Denali and Prothena. © Athira Pharma, Inc. All Rights Reserved. 9    

Investment Highlights Late-stage program fosgonimeton (ATH-1017) designed to Our novel small enhance Hepatocyte Growth Factor (HGF) and its receptor, molecule compounds are MET designed to act on a • Well established HGF/MET pathway is critical to normal brain function and is compromised naturally occurring in Alzheimer’s disease (AD) and other neurological diseases mechanism to repair and restore neuronal health • Topline data for Phase 2 ACT-AD clinical trial expected by end of 2Q22 • Phase 3 LIFT-AD clinical trial expected to complete enrollment in 3Q22 with topline data Potentially pivotal program in expected in 1H23 Alzheimer’s with a growing pipeline • Compelling Phase 1 data in AD demonstrated statistically significant improvement addressing neurodegenerative (p=0.027) of ERP P300 latency, an objective measure of working memory processing speed and neuropsychiatric indications • Cognitive improvement in Alzheimer’s disease is a multi-billion dollar market opportunity Strong balance sheet Leadership team with significant to support clinical programs CNS product development and through key inflection points approval experience © Athira Pharma, Inc. All Rights Reserved. 10    

Therapeutic Potential Across a Broad Range of Clinical Applications P RE CL INICAL CL INICA L Discovery and Status and Anticipated Program Indication Phase 1 Phase 2 Phase 3 Development Upcoming Milestones Open-Label LIFT-AD enrollment Phase 3 Clinical Trial complete 3Q22; Extension topline data 1H23 Alzheimer’s Disease Open-Label ACT-AD topline Fosgonimeton Phase 2 Clinical Trial Extension data by end of 2Q22 (subcutaneous) Parkinson’s Disease SHAPE first patient Dementia and Dementia Phase 2 Clinical Trial dosed 1Q22 with Lewy Bodies Neuropsychiatric First subject dosed ATH-1020 (oral) Phase 1 Clinical Trial Indications 1Q22 Ongoing IND-enabling ATH-1019 (oral) Peripheral Indications studies © Athira Pharma, Inc. All Rights Reserved. 11    

Alzheimer’s Disease Has Significant Market Potential 35 million Over 100 million 6.2 million treatment eligible globally by 2050 patients in the US in 2021 based People living with Alzheimer’s dementia today1 ~900,000 new patients on prevalence data diagnosed annually in the US alone1,2 Growing at 3% per year2,3 Multi-Billion $ Market Despite generic entries Significant opportunity for Mild to Moderate comprises 81% fosgonimeton of all patients with Only One Market research suggests favorable reaction Alzheimer’s Disease and receptivity to fosgonimeton base case New product (Aduhelm™) 78.5% of these patients target product profile as a potential first-line launched since 2003 receive Rx therapies3,4 therapy to improve cognition5 1 https://www.who.int/news—room/factroom/fact—sheets/detail/dementia. 2 https://www.alz.org/media/documents/alzheimers-facts-and-figures.pdf. 3 GlobalData AD prevalence data access and analysis. 4 https://www.nia.nih.gov/news/half-alzheimers-disease-cases-may-be-mild. 5 ClearView Healthcare Partners Market Research Analysis. © Athira Pharma, Inc. All Rights Reserved. 12    

Additional Large Market Potential in Parkinson’s Disease and Lewy Body Dementia Nearly 1 million DLB is the third most $51.9B people in the US and more common cause of dementia than 10 million people accounting for 5-15% of all Economic burden of PD globally are living with overall in the US, as of 20174 dementia cases globally2,4 Parkinson’s disease (PD)1 ~50% PDD and DLB are both types Significant opportunity of PD patients experience of Lewy body disorder, dementia symptoms2,4 for fosgonimeton differentiated by onset of dementia symptoms relative to PD diagnosis3 Initial market research suggests Only One fosgonimeton base case target TYPES OF LEWY BODY DISORDER product profile has the potential treatment option for to address an overlooked and dementia symptoms of PD1,3 DLB PDD underserved PDD and DLB Dx 1 year patient population5 post-Dx 1 year post-Dx 1 https://www.parkinson.org/Understanding-Parkinsons. 2 https://www.alz.org/alzheimers-dementia/what-is-dementia/types-of-dementia. 3 Galasko, Neurol Clin 2017. 4 Yang et al, NPJ Parkinsons Dis 2020. 5 ClearView Healthcare Partners Market Research Analysis. © Athira Pharma, Inc. All Rights Reserved. 13

Our Novel Approach to Brain Health: Positively Augmenting the HGF/MET System MET is one of the most stably expressed genes in the adult human brain Stable MET expression is a signature of the healthy adult brain1 Fosgonimeton positively modulates HGF/MET • Small molecule prodrug that is immediately converted to an active metabolite (Fosgo-AM) in plasma • Crosses the blood-brain barrier Neural Network Neurotransmitter Neuron Health • Positively modulates HGF/MET Support Modulation Synaptogenesis Regeneration Synaptic current • Administered via subcutaneous injection Neurogenesis Survival Synaptic localization Neurite outgrowth Anti-inflammation Long-term potentiation 1 Hawrylycz et al, Nature Neuroscience 2015 HGF/MET signaling and downstream effects described in: Desole et al, Frontiers in Cell and Dev Bio 2021 Funakoshi and Nakamura, Current Signal Transduction Therapy 2011 © Athira Pharma, Inc. All Rights Reserved. 14    

Fosgonimeton Has Achieved Early Proof of Concept in Phase 1 N=11 Randomized, Placebo, Fosgonimeton (40 mg) Subcutaneous, Daily, 8 days ERP OBSERVATIONS ERP analysis to-date suggests treatment effects on P300 latency in AD subjects • Gradual decrease in latency over time in the treated group (N=7) • Short-term, rapid improvements are indicative of neurotransmitter, NMDA receptor modulation    • Lasting effects may be indicative of connectivity and structural improvements P300 LATENCY: ACTIVE v PLACEBO TREATED AD SUBJECTS Fosgonimeton 0 (ms) -20 Latency -40 P300     -60 Decreased latency on pre-dose recordings (arrows) taken 24 hours after the last dose on the previous day may be -80 (73) ms indicative of sustained improvement Significant change from baseline observed on Day 8 Note: P300 data from FZ, CZ, and PZ electrodes. Data plotted as mean +/- SE. *p=0.027 with MMRM. © Athira Pharma, Inc. All Rights Reserved. 15    

Achieving Target Milestones and Executing with Strength for the Future

Athira is Successfully Progressing its Business Achieving targeted milestones and well-positioned for the future 1ï’ Executed against the company’s strategic priorities and poised to report topline results from the Phase 2 ACT-AD study by the end of the Effective and second quarter of 2022 Experienced ï’ Systematically and thoughtfully added experience and expertise to our board and management team in support of advancing our strategy Leadership Teamï’ Experience overseeing both approval and commercialization of novel therapeuticsï’ Prudent balance sheet management and strategic allocation of capital 2 Initiated an open label extension of our LIFT-AD ï’ and ACT-AD trials to allow all eligible patients to receive treatment with fosgonimeton for up to an additional 26 weeksï’ Completed enrollment of 77 patients in our ACT-AD study in October 2021, with topline data expected by the end of 2Q22ï’ Targeting full enrollment of the LIFT-AD Phase 3 study for 3Q22, with topline data expected in the first half of 2023. The company opportunistically increased the sample size of the LIFT-AD study to strengthen the statistical power of key co-secondary endpoints and Executed on Lead enhance the potential for a single pivotal clinical study Candidateï’ Dosed first patient in our SHAPE Phase 2 clinical trial of fosgonimeton in Parkinson’s disease dementia and Dementia with Lewy bodiesï’ Presented preclinical data that demonstrated that the mechanism of action of the active metabolite of fosgonimeton is through positive modulation of HGF/MET ’ Presented baseline Event Related Potential (ERP) P300 latency data from our ACT-AD study at the AD/PD™ conference that showed that the study patient population enrolled in the Phase 2 trial is representative of the mild-to-moderate AD population and is appropriate to evaluate the effects of fosgonimeton on ERP P300 latency 3ï’ Launched a Phase 1 clinical trial for ATH-1020, our novel, orally available, brain-penetrant small molecule, after receiving U.S. Food and Drug Administration clearance for the Investigational New Drug application in January 2022 Progressed ï’ Presented preclinical data at the American Society for Experimental Neurotherapeutics (ASENT) showing that ATH-1020 demonstrated Pipeline neuroprotective effects, mitigated depression-like behaviors and rescued mismatch negativity response, a translatable measure of event-related potential that shows consistent and robust deficits in both rodent models and schizophrenia patients © Athira Pharma, Inc. All Rights Reserved. 17    

1 Competitive Strength: Experienced and Proven Management Team Years of C-suite / Exec. Clinical CNS Experience Experience Experience Development Experience Mark Litton • Has been with Athira since joining as COO in 2019 President and CEO • Previously served as President and COO of Alpine Immune Sciences 25+ • Prior to Alpine, spent 14 years at Alder Biopharmaceuticals, where he was co-founder and CBO directly responsible for raising ~$1B in equity capital and led negotiations for numerous corporate alliances with biotech and pharmaceutical companies prior to its sale to Lundbeck for ~$2B Rachel Lenington • Extensive strategic and operational leadership experience in drug development, commercialization and launch COO • Played an instrumental role in the development of, and multiple global approvals and launches for, Prolia®, ADCETRIS®, PADCEV®, and TUKYSA® at Amgen and Seagen 20+ • Also drove drug, vaccine and diagnostic development and approvals for neglected diseases at the Bill & Melinda Gates Foundation Hans Moebius • Previously co-founded Exciva GmbH and served as its Chief Executive Officer and Chief Medical Officer CMO • Also served as scientific advisory board member and Chief Medical Officer at Rodin Therapeutics 30+ • Prior to that, he served as Executive Vice President of Clinical Research at CHASE Pharmaceuticals Glenna Mileson • Has broad industry experience with companies of all sizes from small, privately owned businesses to large, publicly traded CFO companies. 25+ • Previously served as the Chief Financial Officer for Pregenen, a biotech company developing gene editing and cell signaling technologies Kevin Church • Has been a bench scientist for several small biotechnology companies EVP, Research • Has held several positions at Athira including Senior Research Scientist, Director, and Vice President of Discovery 10+• Expertise in the translational biomarker ERP P300 Mark Worthington • Has advised private and public life sciences and other companies on a wide range of strategic business and legal matters General Counsel • Previously practiced corporate and securities law at Summit Law Group where he chaired the corporate/securities practice and 25+ served as the co-managing partner Simon Daggett • Brings more than 30 years drug development experience, including 19 years at Allergan VP Clinical 30+ Operations • Has considerable global expertise leading all aspects of clinical studies from pre-IND through Phase 3 to approval Lana Gloukhova M.D, VP Drug • Has a proven track record leading global safety and clinical teams at multinational pharmaceutical companies including CSL 30+ Safety and Behring, AbbVie, Merck and Schering-Plough Pharmacovigilance © Athira Pharma, Inc. All Rights Reserved. 18    

1 Competitive Strength: Dr. Litton is the Right Leader for Athira Lifetime of Experience in Biotechnology > Executive Leadership—Chief Operating Officer of Athira from June 2019 to October 2021. President and Chief Operating Officer of Alpine Immune Sciences from August 2018 to April 2019. Chief Business Officer of Alder Biopharma from 2004 to 2018 > Strategic Navigation—At Alder, directly responsible for raising over ~$1B in equity capital and led negotiations for numerous corporate alliances between biotech and pharmaceutical companies until successfully sold to Lundbeck A/S in October 2019 > Clinical Development—At Athira, has overseen progression of ATH-1017 to Phase 3 > Commercialization—Vice President of Business Development for Celltech Group, responsible for securing, commercializing and partnering on numerous novel discoveries and therapeutic programs > Scientific Background—PhD in immunology from Stockholm University, an MBA from Santa Clara University and a BA in Biochemistry and Molecular Biology from UC Santa Cruz > Board Experience—Board Member of Lumen Bioscience since October 2020 Dr. Mark Litton Experienced Executive Commercial Skillset Clinical Background © Athira Pharma, Inc. All Rights Reserved. 19    

2 Competitive Strength: Continued Progression of the Fosgonimeton Phase 2 Trial (ACT-AD) PROOF-OF-CONCEPT TRIAL TO HELP BETTER UNDERSTAND NATURE OF NOVEL INTERVENTION POPULATION TRE ENDPOINTS AND TIMELINE ACT-AD: N=77 (recruitment complete) PRIMARY ENDPOINT mild-to-moderate AD dementia subjects 26-week randomized, double-blind treatment, • Change of P300 latency (55-85 years; CDR 1 and 2; MMSE 14-24 incl.) + optional 26-week OLEX • Safety SECONDARY ENDPOINTS Potential Pathways to success: Fosgonimeton (70 mg) • Cognition: ADAS-Cog11 • Achieves statistical significance on • Global clinical change: ADCS CGIC—Clinician primary endpoint Function: ADCS-ADL23 • • Key secondary endpoints trending Randomization (1:1:1) TIMELINE • Functions as interim analysis for • Topline data expected by end of 2Q22 LIFT-AD without statistical penalty Successfully completed enrollment in October 2021 Topline data expected by end of 2Q22 © Athira Pharma, Inc. All Rights Reserved. 20    

2 Competitive Strength: Key Strategic Decisions to Conduct and Increase Fosgonimeton Phase 3 Trial (LIFT-AD) TRIAL MAY PROVIDE PIVOTAL EVIDENCE TO SUPPORT PRODUCT REGISTRATION POPULATION TRE ENDPOINTS AND TIMELINE LIFT-AD: Target N=~420 PRIMARY ENDPOINT mild-to-moderate AD dementia subjects 26-week randomized, double-blind treatment, • Global Statistical Test (GST) – unbiased (55-85 years; CDR 1 and 2; MMSE 14-24 incl.) + optional 26-week OLEX composite, fed by data from two key secondaries • Safety SECONDARY ENDPOINTS Potential Pathways to success: Fosgonimeton (70 mg) • Cognition: ADAS-Cog11 • Global clinical change: ADCS CGIC—Clinician • Achieves statistical significance on primary endpoint • Function: ADCS-ADL23 • Achieves statistical significance on Randomization (1:1:1) TIMELINE two key secondary endpoints, which • Complete enrollment expected 3Q22 may support approval with a single • Topline data expected 1H23 pivotal study Strong enrollment to-date © Athira Pharma, Inc. All Rights Reserved. 21    

2 Competitive Strength: Executing on Our Phase 2 Trial in PDD and DLB PROOF-OF-CONCEPT TRIAL TO UNDERSTAND THE POTENTIAL OF ATH-1017 BEYOND ALZHEIMER’S DISEASE POPULATION TREATMENT DURATION ENDPOINTS AND TIMELINE PRIMARY ENDPOINT N=~75 mild-to-moderate 26-week randomized, • Global Statistical Test (combining P300 and PDD or DLB subjects double-blind treatment ADAS-Cog13) (MOCA 11-23 at baseline) • Safety SECONDARY ENDPOINTS Fosgonimeton (70 mg) • P300 Latency • Cognition: ADAS-Cog13 Potential Pathways to success: • Global clinical change: ADCS CGIC—Clinician • Achieves statistical significance on • Function: ADCS-ADL23 primary endpoint • Motor Function: MDS-UPDRS (Exploratory) Randomization (1:1:1) • Shows trends on either cognition TIMELINE and/or motor function • First patient dosed 1Q22    • Actively enrolling First patient dosed in Phase 2 SHAPE trial 1Q22 © Athira Pharma, Inc. All Rights Reserved. 22    

3 Competitive Strength: Executed on Our Pipeline by Initiating a Phase 1 Study for ATH-1020 PHYSIOLOGICAL CHANGES IN THE BRAIN AFFECT BEHAVIOR AND EMOTION • Preclinical data demonstrate enhancing HGF/MET activity has Our novel approach is anti-depressant and anxiolytic effects1,2 focused on restoring • Human clinical trials also show an association between reduced neuronal health and HGF/MET expression levels and depression/anxiety3-7 function to repair disruptions in neuronal • ATH-1020 connectivity found in a—A brain-penetrant small molecule positive modulator of HGF/MET variety of neuropsychiatric Demonstrated improvements in depression and schizophrenia in —diseases preclinical animal models—Convenient once-daily oral dosing—Phase 1 first-in-human studies launched, first subject dosed 1Q22 1 Isogawa et al, Neuropsychobiology 2005 4 Ciuculete et al, Epigenetics 2019 6 Russo, Proteomic Insights 2010 2 Wakatsuki et al, Neuropeptides 2007 5 Ramsey et al, PLoS ONE 2016 7 Burdick et al, AM J Psychiatry 2010 3 Russo, Biomarker Insights 2010 © Athira Pharma, Inc. All Rights Reserved. 23    

Achievements and Upcoming Milestones RECENT ACHIEVEMENTS LOOKING AHEAD Enrollment completed for Phase 2 ACT-AD trial in Oct    Phase 2 ACT-AD Trial: Topline data expected by 2021 end of 2Q22 Strong enrollment to-date in Phase 3 LIFT-AD trial    Phase 3 LIFT-AD Trial: Open label extension trial underway for ACT-AD and Complete enrollment expected in 3Q22; LIFT-AD Topline data expected 1H23 First patient dosed in Phase 2 SHAPE trial 1Q22    SHAPE enrollment ongoing First subject dosed with first oral molecule, ATH-1020,    Ongoing IND-enabling studies of ATH-1019 in Phase 1 trial as a potential treatment candidate for in peripheral indications neuropsychiatric indications in 1Q22 Continued to strengthen IP portfolio including issuance of fosgonimeton (ATH-1017) US patent Strong balance sheet – cash of $319.7M as of 12/31/21 and no debt © Athira Pharma, Inc. All Rights Reserved. 24    

We Are Executing on Our Strategy as Articulated at IPO Strategy at IPO Actions / Accomplishments Advance fosgonimeton (ATH-1017) through clinical Phase 2 ACT-AD, Phase 3 LIFT-AD and open-label development for AD extension progressed Expand the development of fosgonimeton to include Phase 2 SHAPE trial for Parkinson’s initiated additional indications and delivery methods Focus on translational and functional endpoints to efficiently ERP P300 applied to ongoing trials develop product candidates Continue developing additional pipeline programs and utilize Successful IND for oral molecule ATH-1020 and our ATH platform for further drug discovery additional IND-enabling studies Optimize the value of fosgonimeton and other candidates in Continuously expanding IP portfolio major markets © Athira Pharma, Inc. All Rights Reserved. 25    

Wall Street Analysts Support Athira’s Potential Analysts see significant upside in Large Opportunity Evidenced by Selected Commentary Stock Price Peak Sales Opportunity Projected Product Sales (Unadjusted) Proj. Sales “We view ATHA’s approach to treating Alzheimer’s disease as differentiated with the potential to Analyst ($ bn) expand to other forms of dementia, which we believe $33.00 the market is missing.” - Analyst D, 21-Apr-2022 $7.3 Analyst A (2037) “The data we’ve seen to-date supports a statistically significant benefit on change in P300 + $21.00 vs. 6.4 latency in the ACT-AD study, as our assessment of the Today Analyst B (2037) available P300 data in Alzheimer’s disease suggests that the Phase 1b results were not random, but rather due to drug effect…” 5.5 - Analyst C, 28-Mar-2022 Analyst C (2037) $11.44 “Underlying our cautiously optimistic view in the backdrop of many failures in the AD space, Athira has 5.4 generated promising EEG data in a small number of Analyst D Alzheimer’s patients…” (2034) - Analyst E, 09-Feb-2022 5.2 Analyst E (2032) “We are confident in Mr. Litton’s leadership expertise, noting his extensive public company Stock Price (Current) Median Analyst Price leadership, including as Chief Business Officer at Target Median $5.5 Alder Pharmaceuticals.”    - Analyst B, 17-Jun-2021 Source: Wall street research and market data as of 22-Apr-2022 Note: Projected sales represent unadjusted product sales. © Athira Pharma, Inc. All Rights Reserved. 26    

Highly Qualified Board with Experience Athira Needs for Pivotal Chapter

Effective and Engaged Board Oversight Executing Successfully Positioning for the Future Navigating Hard Against our Strategy Challenges Directors have the right skills and Actively engaged board: Track record of navigating hard experience needed to support • Guides our highest priority – challenges and fostering Athira at this critical time securing regulatory approval sustainable long-term value for the treatment of Alzheimer’s creation for all shareholders The right board in place to disease (AD) oversee Athira during this pivotal • Oversees pipeline built from chapter our proprietary drug discovery platform © Athira Pharma, Inc. All Rights Reserved. 28    

Distinguished Board with Deep Industry, R&D and Commercialization Expertise and Experience Clinical Regulatory Drug Finance and R e l e va n t S k i l l s Development Approval Process Commercialization Financial Planning Independent director appointed since Mar. 2021 & E x p e ri e n c e: Capital Business Legal and Risk Investment Allocation Development Management Management S t a n d i n g f o r Joseph Edelman (Since May 2020) John Fluke, Jr. (Since Dec. 2014) Grant Pickering (Since Jan. 2022) • Current Position: Founder and CEO, • Current Position: Founder and Chairman, • Current Position: Co-founder, CEO, and E l e c t i o n Perceptive Advisors Fluke Capital Management, L.P. director of Vaxcyte, Inc. (NASDAQ: PCVX) • Other Public Boards: Arya Sciences Acq. Corp • Selected Prior Experience: Previously on • Selected Prior Experience: CEO, Mymetics V (NASDAQ: ARYE); Arya Sciences Acq. Corp. boards of PACCAR Inc. (NASDAQ: PCAR), Corp. (OTC: MYMX); CEO and director, Juvaris IV (NASDAQ: ARYD) CellCyte Genetics Corporation, Cell BioTherapetuics • Selected Investments: Acerta Pharma, Therapeutics, Primus International, American • Other Public Boards: Vaxcyte, Inc. (NASDAQ: Alnylam Pharmaceuticals (NASDAQ: ALNY), Seafoods Group PCVX) Sarepta Therapeutics (NASDAQ: SRPT) O t h e r Kelly Romano (Since Dec. 2020) James Johnson (Since Aug. 2020) Mark Litton, M.B.A., Ph.D. D i r e c t o rs Chairwoman • Selected Prior Experience: Former CFO of (Since Oct. 2021) • Current Position: Founder and CEO, Nohla Therapeutics; NanoString Technologies • Current Position: President and CEO, Athira BlueRipple Capital; Operating Partner, AE (NASDAQ: NSTG); Relypsa (NASDAQ: RLYP); • Selected Prior Experience: President and Industrial Partners ZymoGenetics (NASDAQ: ZGEN); Targeted Chief Operating Officer, Alpine Immune Genetics Sciences (NASDAQ: ALPN); Co-founder and • Selected Prior Experience: Leadership positions in operations, business development, Chief Business Officer, Alder M&A and sales & marketing at United Biopharmaceuticals (NASDAQ: ALDR); Vice Technologies Corp. (NYSE: UTX)1 President of Business Development for Celltech Group • Other Public Boards: UGI (NYSE: UGI); Dorman Products (NASDAQ: DORM) Barbara Kosacz (Since Mar. 2021) Michael Panzara, M.D., M.P.H. (Since Mar. 2022) • Current Position: Chief Operating Officer and • Current Position: Chief Medical Officer and General Counsel, Kronos Bio, Inc. (NASDAQ: Head of Therapeutics Discovery and KRON) Development, Wave Life Sciences (NASDAQ: • Selected Prior Experience: Partner and Head WVE) of the International Life Sciences Practice at • Selected Prior Experience: Head of Multiple Cooley LLP Sclerosis, Neurology and Ophthalmology • Other Public Boards: XOMA Corp (NASDAQ: Therapeutic Areas in Global Development, XOMA); Phoenix Biotech Acq. Corp. (NASDAQ: Sanofi Genzyme (ENXTPA: SAN); Vice PBAX) President and Chief Medical Officer in Neurology, Biogen (NASDAQ: BIIB) 1 Now Carrier Global, Otis Global and Raytheon Technologies. © Athira Pharma, Inc. All Rights Reserved. 29    

Our Highly Qualified Nominees Joseph Edelman John M. Fluke, Jr. Grant Pickering Director Since: May 2020 Director Since: December 2014 Director Since: January 2022 • 20+ years of experience as a highly • 40+ years of executive leadership and • 30+ years of experience across vaccine and respected investor and advisor to small- and board experience at many successful immunotherapeutic drug development and mid-size biotech companies companies commercialization • Grew Perceptive Advisors’ AUM from $6 • Founder and Chairman of Fluke Capital • Led the successful formation and financing million to approximately $9.5 billion Management, L.P. of multiple platform companies, including vaccine innovation company Vaxcyte, Inc. • Track record of success as a board member • Extensive background as an investor in (NASDAQ: PCVX), which he co-founded and and investor in many successful many successful companies where he currently serves as CEO biotechnology companies • Appointed to the board in January 2022 after he was identified to Athira by Mr. Kayne Selected Experience Selected Experience Selected Experience Paramount Capital CellCyte Genetics Asset Management Primus International © Athira Pharma, Inc. All Rights Reserved. 30    

Setting the Facts Straight – The Leen Kawas Investigation • On June 16, 2021, the board determined to place Leen Kawas on temporary leave pending a review of actions stemming from doctoral research that Dr. Kawas conducted while at Washington State University (WSU). The board established an independent special committee to undertake this review. • During the course of its investigation, the special committee, with the assistance of independent outside counsel, determined that Dr. Kawas altered images in her 2011 doctoral dissertation and at least four research papers that she co-authored while she was a graduate student at WSU, and published from 2011 to 2014. • Among its other findings, the special committee found that Athira’s issued U.S. patent claiming ATH-1017, Athira’s lead development candidate, does not cite any paper that the committee found to contain an image altered by Dr. Kawas. • Effective October 18, 2021, Dr. Kawas submitted her resignation as president and chief executive officer of Athira and as a member of the board of directors. • The WSU research misconduct actions are still pending. © Athira Pharma, Inc. All Rights Reserved. 31    

Kayne’s Campaign Not in the Best Interest of All Shareholders

Athira Is Well-Positioned to Continue Executing with Strength; Kayne’s Platform Is Misguided Our Plan Kayne’s “Platform” Progressing Phase 2 ACT-AD clinical trial, Phase 3 LIFT-AD clinical No articulated business or operational platform trial and open-label extension trial ƒ» Gain personal representation for Mr. Kayne on the board Capturing opportunity to expand into additional indications including PDD and DLB Slate of directors who do not bring incremental domain expertise that    Ongoing SHAPE enrollment would enhance our already highly qualified board Ongoing IND-enabling studies of ATH-1019 in peripheral indications Replace our current CEO Maintaining strong balance sheet to support clinical programs Pushed for a substantive role for Dr. Kawas (who is now his business through key inflection points partner) Committed to continuing to build on deep industry, R&D and commercialization expertise of board and leadership Strong, experienced management team Athira Pharma, Inc. All Rights Reserved. 33    

Athira Has Engaged in Good Faith with Kayne; Kayne Has Rejected Our Attempts to Find Common Ground Ongoing Dialogue with • Athira’s directors have had ongoing dialogue with Kayne, including frequent conversations over the last several Kayne months • Athira has been open to shareholder input, including on directors, and interviewed both Grant Pickering and George Bickerstaff, who were identified by Kayne; the board determined Pickering would be additive and appointed Responsiveness to him to the board at Kayne’s suggestion Shareholders • Additionally, in March 2022 the board appointed Michael Panzara, M.D. who brings over 20 years of biopharmaceutical industry experience developing therapies for neurological disorders • The board remains focused on further expanding its deep industry, R&D and commercialization expertise • Athira has proposed multiple paths forward that would enable the company to avoid a costly, distracting proxy Openness to Negotiated contest Resolution • Mr. Kayne has pushed an agenda to appoint himself to the board and terminate our CEO, and also have us resume a relationship with our former CEO, Dr. Kawas • Kayne is attempting to replace our CEO, which the board believes is not in the best interest of all shareholders Dr. Litton – The Right Person to Lead Athira • Dr. Litton has demonstrated exemplary leadership since joining Athira in July 2019, and is the right person to lead our company forward © Athira Pharma, Inc. All Rights Reserved. 34    

Conclusion • Poised to report topline results from Phase 2 ACT-AD study by end of 2Q22 Successfully executing • Expect to complete enrollment for expanded LIFT-AD Phase 3 study by 3Q22, with larger sample size enhancing potential for single pivotal clinical study strategic drug development • Dosed first patient in SHAPE Phase 2 clinical trial of fosgonimeton in Parkinson’s disease dementia and Dementia with Lewy bodies in January 2022; priorities for Alzheimer’s positive results from this proof-of-concept trial would strengthen the potential pan dementia utility of fosgonimeton and increase confidence in the mode of Disease and other dementias action with large patient populations • Launched Phase 1 clinical trial for ATH-1020 that have significant unmet • Successful execution reflected in stock price performance – from the day of public announcement that Dr. Kawas resigned and Dr. Litton was appointed CEO need and market potential (October 21, 2021) through the day that Athira filed its preliminary proxy statement publicly disclosing Mr. Kayne’s director nominations (March 25, 2022), our stock price increased by ~32%, while the SPDR S&P Biotech ETF (XBI) index decreased by ~28% over the same period • CEO Mark Litton, PhD, MBA has 25+ years experience in the biopharma industry, including C-suite roles at 3 publicly traded companies — Previously served as President and COO of Alpine Immune Sciences. Prior to Alpine, spent 14 years at Alder Biopharmaceuticals, where he was co-Strong management team led founder and Chief Business Officer directly responsible for raising ~$1B in equity capital and led negotiations for numerous corporate alliances with by CEO Mark Litton with deep biotech and pharmaceutical companies prior to its sale to Lundbeck for ~$2B industry, R&D and • COO Rachel Lenington, MBA has 20+ years of strategic and operational leadership experience in drug development, commercialization and launch commercialization expertise to drive future shareholder value • Chief Medical Officer Hans Moebius, MD, PhD, ECPM, FAAN is an internationally recognized expert in neuropsychiatry, with 30+ years of experience in drug R&D and regulatory strategy, and has led several CNS projects to successful approval, including Namenda, the second leading AD therapy worldwide • CFO Glenna Mileson has 25+ years of financial and business management experience at biopharmaceutical and other companies The right board with diverse and • Highly qualified, experienced board with the right skills for Athira: clinical development, regulatory approval, commercialization, finance & financial planning, curated skillsets to oversee capital allocation, BD, legal & risk management and investment management Athira’s growth during pivotal • Record of systematically and thoughtfully adding experience and expertise, including 2 new independent directors YTD in 2022 and 3 in the past year chapter Mr. Kayne’s self-serving • Mr. Kayne has rebuffed multiple attempts by our board to constructively engage in order to avoid a costly, unnecessary proxy contest campaign is misguided and • Mr. Kayne has pushed an agenda to appoint himself to the board and terminate our CEO, and also have us resume a relationship with our former CEO, Dr. detrimental to the interests of Kawas all shareholders • Messrs. Kayne and Bickerstaff are generalists; they do not add to the skills that are already well represented on the board This proxy contest is a needless distraction at a time when Athira should be focused on delivering the results of the Phase 2 ACT-AD study © Athira Pharma, Inc. All Rights Reserved. 35    

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