<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-07-23</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001528115</issuerCik>
        <issuerName>Annexon, Inc.</issuerName>
        <issuerTradingSymbol>ANNX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001703031</rptOwnerCik>
            <rptOwnerName>Bain Capital Life Sciences Investors, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>200 CLARENDON STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001703030</rptOwnerCik>
            <rptOwnerName>Bain Capital Life Sciences Partners, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>200 CLARENDON STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001687968</rptOwnerCik>
            <rptOwnerName>Bain Capital Life Sciences Fund, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>200 CLARENDON STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001702921</rptOwnerCik>
            <rptOwnerName>BCIP Life Sciences Associates, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>200 CLARENDON STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001578965</rptOwnerCik>
            <rptOwnerName>Koppel Adam</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BAIN CAPITAL LIFE SCIENCES INVESTORS</rptOwnerStreet1>
            <rptOwnerStreet2>LLC, 200 CLARENDON STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001702957</rptOwnerCik>
            <rptOwnerName>Schwartz Jeffrey Lawrence</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BAIN CAPITAL LIFE SCIENCES INVESTORS</rptOwnerStreet1>
            <rptOwnerStreet2>LLC, 200 CLARENDON STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>22222221</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series D Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2812543</value>
                    <footnoteId id="F2"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares of Series C Preferred Stock will automatically convert on a 1-for-8.81 basis into Common Stock immediately prior to the closing of the Issuer's initial public offering.</footnote>
        <footnote id="F2">The shares of Series D Preferred Stock will automatically convert on a 1-for-8.81 basis into Common Stock immediately prior to the closing of the Issuer's initial public offering.</footnote>
        <footnote id="F3">Represents 20,158,775 shares of Series C Preferred Stock held of record by Bain Capital Life Sciences Fund, L.P. (&quot;BCLS&quot;) and 2,063,446 shares of Series C Preferred Stock held of record by BCIP Life Sciences Associates, LP (&quot;BCIPLS&quot; and, together with BCLS, the &quot;Bain Capital Life Sciences Entities&quot;).</footnote>
        <footnote id="F4">Represents 2,551,384 shares of Series D Preferred Stock held of record by BCLS and 261,159 shares of Series D Preferred Stock held of record by BCIPLS.</footnote>
        <footnote id="F5">Bain Capital Life Sciences Partners, LP (&quot;BCLSP&quot;) is the general partner of BCLS. As a result, BCLSP may be deemed to share voting and dispositive power with respect to the securities held by BCLS. BCLSP disclaims beneficial ownership of such securities except to the extent of their pecuniary interest therein.</footnote>
        <footnote id="F6">Bain Capital Life Sciences Investors, LLC (&quot;BCLSI&quot;), whose managers are Jeffrey Schwartz and Adam Koppel, is the general partner of BCLSP and governs the investment strategy and decision-making process with respect to investments held by BCIPLS, whose general partner is Boylston Coinvestors, LLC. As a result, each of BCLSI, Mr. Schwartz and Dr. Koppel may be deemed to share voting and dispositive power over the shares held by the Bain Capital Life Sciences Entities. BCLSI, Mr. Schwartz and Dr. Koppel each disclaim beneficial ownership of such securities except to the extent of their pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>BAIN CAPITAL LIFE SCIENCES INVESTORS, LLC, By: /s/ Jeffrey Schwartz, Name: Jeffrey Schwartz, Title: Managing Director</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BAIN CAPITAL LIFE SCIENCES PARTNERS, LP, By: Bain Capital Life Sciences Investors, LLC, its general partner, By: /s/ Jeffrey Schwartz, Name: Jeffrey Schwartz, Title: Managing Director</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BAIN CAPITAL LIFE SCIENCES FUND, L.P., By: Bain Capital Life Sciences Partners, LP, its general partner, By: Bain Capital Life Sciences Investors, LLC, its general partner, By: /s/ Jeffrey Schwartz, Name: Jeffrey Schwartz, Title: Managing Director</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BCIP LIFE SCIENCES ASSOCIATES, LP, By: Boylston Coinvestors, LLC, its general partner, By: /s/ Jeffrey Schwartz, Name: Jeffrey Schwartz, Title: Authorized Signatory</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Adam Koppel</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jeffrey Schwartz</signatureName>
        <signatureDate>2020-07-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
