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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2017-12-07</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001714899</issuerCik>
        <issuerName>Denali Therapeutics Inc.</issuerName>
        <issuerTradingSymbol>DNLI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001605598</rptOwnerCik>
            <rptOwnerName>ARCH Venture Fund VIII, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ARCH VENTURE PARTNERS VIII, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>8755 W. HIGGINS ROAD, SUITE 1025</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60631</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001616165</rptOwnerCik>
            <rptOwnerName>ARCH Venture Partners VIII, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ARCH VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>8755 W. HIGGINS ROAD, SUITE 1025</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60631</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001616176</rptOwnerCik>
            <rptOwnerName>ARCH Venture Partners VIII, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ARCH VENTURE PARTNERS VIII, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>8755 W. HIGGINS ROAD, SUITE 1025</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60631</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001219039</rptOwnerCik>
            <rptOwnerName>CRANDELL KEITH</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ARCH VENTURE PARTNERS VIII, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>8755 W. HIGGINS ROAD, SUITE 1025</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60631</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001219043</rptOwnerCik>
            <rptOwnerName>BYBEE CLINTON</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ARCH VENTURE PARTNERS VIII, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>8755 W. HIGGINS ROAD, SUITE 1025</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60631</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>312500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-1 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>10068749</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>375000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>312500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares are directly held by ARCH Venture Fund VIII, L.P. (&quot;ARCH VIII&quot;). ARCH Venture Partners VIII, L.P. (the &quot;GPLP&quot;), as the sole general partner of ARCH VIII, may be deemed to beneficially own certain of the shares held by ARCH VIII. ARCH Venture Partners VIII, LLC (&quot;GPLLC&quot;), as the sole general partner of GPLP, may be deemed to beneficially own the shares held by ARCH VIII. The GPLP and GPLLC disclaim beneficial ownership of such shares except to the extent of any pecuniary interest therein. Keith Crandell and Clinton Bybee, as managing directors of GPLLC, may be deemed to beneficially own the shares held by ARCH VIII. Messrs. Crandell and Bybee disclaim beneficial ownership of such shares except to the extent of any pecuniary interest therein.</footnote>
        <footnote id="F2">The Series A-1 Preferred Stock shall automatically convert into shares of Common Stock on a 1:1 basis immediately prior to the completion of
the Issuer's initial public offering of Common Stock and has no expiration date.</footnote>
        <footnote id="F3">The Series A-2 Preferred Stock shall automatically convert into shares of Common Stock on a 1:1 basis immediately prior to the completion of
the Issuer's initial public offering of Common Stock and has no expiration date.</footnote>
        <footnote id="F4">The Series B-1 Preferred Stock shall automatically convert into shares of Common Stock on a 1:1 basis immediately prior to the completion of
the Issuer's initial public offering of Common Stock and has no expiration date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>ARCH Venture Partners VIII, LLC By: /s/ Mark McDonnell, Attorney-in-Fact</signatureName>
        <signatureDate>2017-12-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>ARCH Venture Fund VIII, L.P. By: ARCH Venture Partners VIII, L.P. By: /s/ Mark McDonnell, Attorney-in-Fact</signatureName>
        <signatureDate>2017-12-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>ARCH Venture Partners VIII, L.P. By: ARCH Venture Partners VIII, LLC By: /s/ Mark McDonnell, Attorney-in-Fact</signatureName>
        <signatureDate>2017-12-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark McDonnell, as Attorney-in-Fact for Keith Crandell</signatureName>
        <signatureDate>2017-12-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark McDonnell, as Attorney-in-Fact for Clinton Bybee</signatureName>
        <signatureDate>2017-12-07</signatureDate>
    </ownerSignature>
</ownershipDocument>
