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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2010-11-15</periodOfReport>

    <dateOfOriginalSubmission>2010-11-15</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001389545</issuerCik>
        <issuerName>NovaBay Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>NBY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001236257</rptOwnerCik>
            <rptOwnerName>WU ROY J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O NOVABAY PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>5980 HORTON STREET, SUITE 550</rptOwnerStreet2>
            <rptOwnerCity>EMERYVILLE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94608</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP Bus &amp; Corp Development</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.89</value>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2010-11-15</value>
                <footnoteId id="F2"/>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>40000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2011-11-15</value>
            </exerciseDate>
            <expirationDate>
                <value>2020-11-14</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>40000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>190000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Original Form 4 filed on November 15, 2010. This amendment is filed to correct the exercise price from $1.85 to $1.89 per share.</footnote>
        <footnote id="F2">Original Form 4 filed on November 15, 2010. This amendment is filed to correct the grant date from November 12, 2010 to November 15, 2010, the date the last signature to the Board Written Consent granting the options was received by the Company.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Theresa Granados, as Attorney-in-Fact for Roy Wu</signatureName>
        <signatureDate>2010-11-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
