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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2017-03-01</periodOfReport>

    <dateOfOriginalSubmission>2017-03-02</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001478121</issuerCik>
        <issuerName>Pfenex Inc.</issuerName>
        <issuerTradingSymbol>PFNX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001612843</rptOwnerCik>
            <rptOwnerName>Lucy Patrick K.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PFENEX INC., 10790 ROSELLE STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.47</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-03-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>11238</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-03-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11238</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>11238</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This amendment is being filed to correct the total number of derivative securities acquired in connection with the Option.</footnote>
        <footnote id="F2">1/24th of the total shares subject to the Option shall vest every month after the date of grant such that all shares shall be fully vested on the two year anniversary of the Vesting Commencement Date. &quot;Vesting Commencement Date&quot; shall mean March 1, 2017.</footnote>
    </footnotes>

    <remarks>Interim CEO, President and Secretary, and Chief Business Officer</remarks>

    <ownerSignature>
        <signatureName>/s/ Patricia Lady, as Attorney-in-Fact</signatureName>
        <signatureDate>2017-03-16</signatureDate>
    </ownerSignature>
</ownershipDocument>
