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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-12-21</periodOfReport>

    <notSubjectToSection16>0</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>0001723842</rptOwnerCik>
            <rptOwnerName>Neuro Line Partners LP</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>0001723787</rptOwnerCik>
            <rptOwnerName>Bratton Capital Management, 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>0001723783</rptOwnerCik>
            <rptOwnerName>Bratton Capital 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>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2020-12-21</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>383411</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Neuro Line Partners, L.P.</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>12201634</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By AKDL, L.P.</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Represents a pro rata in-kind distribution of shares of common stock of Denali Therapeutics Inc. from Neuro Line Partners, L.P. (&quot;Neuro Line&quot;) to limited partners of Neuro Line without consideration, including to an entity controlled by Douglas K. Bratton.</footnote>
        <footnote id="F2">These shares of common stock of the Issuer were held directly by Neuro Line Partners, L.P. (&quot;Neuro Line&quot;).  The general partner of Neuro Line is Bratton Capital Management, L.P. (&quot;Bratton Capital Management&quot;).  The general partner of Bratton Capital Management is Bratton Capital, Inc. (&quot;Bratton Capital&quot;).  Douglas K. Bratton is the sole director of Bratton Capital.  Neuro Line is ultimately controlled by Mr. Bratton and Mr. Bratton had voting and investment power over all securities that were held by Neuro Line.</footnote>
        <footnote id="F3">(Continued from footnote 2) In addition, Bratton Capital Management, Bratton Capital, and Mr. Bratton may have been deemed to have had a pecuniary interest in a portion of the securities that were held by Neuro Line due to Bratton Capital Management's right to receive performance-based allocations and Bratton Capital Management and Mr. Bratton may have been deemed to have had a pecuniary interest in a portion of the securities that were held by Neuro Line through direct or indirect limited partner and/or general partner interests in Neuro Line.  Bratton Capital Management, Bratton Capital and Mr. Bratton may each have been deemed to beneficially own the securities held by Neuro Line.  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="F4">These shares of common stock of the Issuer 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="F5">(Continued from footnote 4) 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>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>DOUGLAS K. BRATTON, Name: /s/ Douglas K. Bratton</signatureName>
        <signatureDate>2020-12-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>NEURO LINE PARTNERS, L.P., By:  Bratton Capital Management, L.P., its general partner, By:  Bratton Capital, Inc., its general partner, Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2020-12-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BRATTON CAPITAL MANAGEMENT, L.P., By:  Bratton Capital, Inc., its general partner, Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2020-12-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BRATTON CAPITAL, INC., Name: /s/ Douglas K. Bratton, Title: Sole Director</signatureName>
        <signatureDate>2020-12-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
