<?xml version="1.0" encoding="US-ASCII"?>
<!-- Generated by CompSci Transform (tm) - http://www.compsciresources.com -->
<!-- Created: Mon Apr 14 20:30:00 UTC 2025 -->
<xs:schema elementFormDefault="qualified" xmlns:atha="http://www.athira.com/20250529" targetNamespace="http://www.athira.com/20250529" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:us-types="http://xbrl.us/us-types/2009-01-31" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:dtr="http://www.xbrl.org/dtr/type/2022-03-31" xmlns:xbrli="http://www.xbrl.org/2003/instance">
  <xs:annotation>
    <xs:appinfo>
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      <link:linkbaseRef xlink:type="simple" xlink:href="atha-20250529_pre.xml" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef"/>
      <link:linkbaseRef xlink:type="simple" xlink:href="atha-20250529_def.xml" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef"/>
    </xs:appinfo>
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  <xs:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd"/>
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  <xs:import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/ecd/2024" schemaLocation="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/dei/2024" schemaLocation="https://xbrl.sec.gov/dei/2024/dei-2024.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2009/role/negated" schemaLocation="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd"/>
  <xs:import namespace="http://www.xbrl.org/dtr/type/2022-03-31" schemaLocation="https://www.xbrl.org/dtr/type/2022-03-31/types.xsd"/>
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  <xs:import namespace="http://xbrl.sec.gov/dei-sub/2024" schemaLocation="https://xbrl.sec.gov/dei/2024/dei-sub-2024.xsd"/>
  <xs:import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd"/>
  <xs:element name="KevinChurchMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="atha_KevinChurchMember"/>
  <xs:element name="MarkLittonMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="atha_MarkLittonMember"/>
  <xs:element name="MarkWorthingtonMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="atha_MarkWorthingtonMember"/>
</xs:schema>
