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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2021-02-12</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001281933</rptOwnerCik>
            <rptOwnerName>BRATTON DOUGLAS K</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>201 MAIN STREET, SUITE 1900</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716958</rptOwnerCik>
            <rptOwnerName>AKDL, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>201 MAIN STREET, SUITE 1900</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001626597</rptOwnerCik>
            <rptOwnerName>Crestline SI (GP), L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>201 MAIN STREET, SUITE 1900</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001626596</rptOwnerCik>
            <rptOwnerName>Crestline Investors, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>201 MAIN STREET, SUITE 1900</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76102</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001536054</rptOwnerCik>
            <rptOwnerName>Crestline Management, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>201 MAIN STREET, SUITE 1900</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>FORT WORTH</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>76201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2021-02-12</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2216798</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>65.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>9984836</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By AKDL, L.P.</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>100102</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Bratton Family Partners L.P.</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares of common stock of Denali Therapeutics Inc. (the &quot;Issuer&quot;) are held directly by AKDL, L.P. (&quot;AKDL&quot;).  The general partner of AKDL is Crestline SI (GP), L.P. (&quot;Crestline SI&quot;) and the investment manager of AKDL is Crestline Management, L.P. (&quot;Crestline Management&quot;).  Crestline Investors, Inc. (&quot;Crestline&quot;) is the general partner of both Crestline SI and Crestline Management.  Douglas K. Bratton is the sole director of Crestline.  AKDL is ultimately controlled by Mr. Bratton and Mr. Bratton has voting and investment power over all securities held by AKDL.  In addition, Crestline SI, Crestline and Mr. Bratton may be deemed to have a pecuniary interest in a portion of the securities held by AKDL through direct or indirect limited partner interests, including limited partner profit interests, and/or general partner interests in AKDL.  Crestline SI, Crestline Management, Crestline and Mr. Bratton may each be deemed to beneficially own the securities held by AKDL.</footnote>
        <footnote id="F2">(Continued from footnote 1) Each such entity and Mr. Bratton disclaims beneficial ownership of such securities except to the extent of its or his respective pecuniary interest therein.</footnote>
        <footnote id="F3">These shares of common stock of the Issuer are held directly by Bratton Family Partners L.P., an entity controlled by Douglas K. Bratton.  Such shares of common stock of the Issuer held by Bratton Family Partners L.P. were received in a previously reported pro rata in-kind distribution from Neuro Line Partners, L.P. without a change in pecuniary interest.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>DOUGLAS K. BRATTON






Name: /s/ Douglas K. Bratton</signatureName>
        <signatureDate>2021-02-17</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>AKDL, L.P., By: Crestline SI (GP), L.P., its general partner, By: Crestline Investors, Inc., its general partner, Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2021-02-17</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>CRESTLINE SI (GP), L.P., By: Crestline Investors, Inc., its general partner, Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2021-02-17</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>CRESTLINE INVESTORS, INC., Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2021-02-17</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>CRESTLINE MANAGEMENT, L.P., By:  Crestline Investors, Inc., its general partner, Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2021-02-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
