<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2022-02-14T07:52:33.8457+00:00 -->
<!-- Copyright (c) 2022 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<xsd:schema targetNamespace="http://biodesix.com/20220214" attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:enum2="http://xbrl.org/2020/extensible-enumerations-2.0" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:us-gaap="http://fasb.org/us-gaap/2021-01-31" xmlns:dei="http://xbrl.sec.gov/dei/2021q4" xmlns:bdsx="http://biodesix.com/20220214" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xlink="http://www.w3.org/1999/xlink">
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/instance"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/linkbase"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" namespace="http://xbrl.org/2005/xbrldt"/>
  <xsd:import schemaLocation="https://xbrl.sec.gov/dei/2021q4/dei-2021q4.xsd" namespace="http://xbrl.sec.gov/dei/2021q4"/>
  <xsd:import schemaLocation="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd" namespace="http://fasb.org/us-gaap/2021-01-31"/>
  <xsd:annotation>
    <xsd:appinfo>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="bdsx-20220214_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:title="Labels link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="bdsx-20220214_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:title="Presentation link" xlink:type="simple"/>
      <link:roleType roleURI="http://biodesix.com/20220214/taxonomy/role/Role_DocumentDocumentAndEntityInformation" id="Role_DocumentDocumentAndEntityInformation">
        <link:definition>100000 - Document - Document And Entity Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xsd:appinfo>
  </xsd:annotation>
</xsd:schema>
