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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-02-07</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001364885</issuerCik>
        <issuerName>Spirit AeroSystems Holdings, Inc.</issuerName>
        <issuerTradingSymbol>SPR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001645009</rptOwnerCik>
            <rptOwnerName>Lohmeier Michelle</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SPIRIT AEROSYSTEMS HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3801 SOUTH OLIVER</rptOwnerStreet2>
            <rptOwnerCity>WICHITA</rptOwnerCity>
            <rptOwnerState>KS</rptOwnerState>
            <rptOwnerZipCode>67210</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP &amp; GM, Airbus Programs</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Class A Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-02-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>F</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2421</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>56.63</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>30015</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Class A Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-02-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8641</value>
                    <footnoteId id="F3"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>38656</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Constitutes shares withheld by the Issuer to satisfy the Reporting Person's withholding tax obligations in connection with the vesting of shares granted to the Reporting Person under the Issuer's Long Term Incentive Plan.</footnote>
        <footnote id="F2">The price reported reflects an average of the high and low trading prices on February 7, 2017, the vesting date.</footnote>
        <footnote id="F3">Restricted stock award. These shares will vest annually at a rate of 33% beginning on February 7, 2018, if the Reporting Person continues to be employed by the Issuer or any of its subsidiaries on each annual vesting date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Joseph T. Boyle, as attorney-in-fact for Michelle Lohmeier</signatureName>
        <signatureDate>2017-02-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
