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

    <schemaVersion>X0304</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2012-01-03</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001396033</issuerCik>
        <issuerName>Lumber Liquidators Holdings, Inc.</issuerName>
        <issuerTradingSymbol>LL</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001186527</rptOwnerCik>
            <rptOwnerName>GRIFFITHS JEFFREY W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O LUMBER LIQUIDATORS HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3000 JOHN DEERE ROAD</rptOwnerStreet2>
            <rptOwnerCity>TOANO</rptOwnerCity>
            <rptOwnerState>VA</rptOwnerState>
            <rptOwnerZipCode>23168</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Advisor</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-03</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>103000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>7.83</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>113000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-03</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>103000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.6814</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-04</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>17000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>7.83</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>27000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-01-04</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>17000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.3610</value>
                    <footnoteId id="F5"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to purchase)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.83</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2012-01-03</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>103000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-10-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>103000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>150672</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to purchase)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.83</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2012-01-04</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>17000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-10-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>17000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>133672</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The sale of these shares was effectuated pursuant to a Rule 10b5-1 trading plan adopted by the reporting person on November 8, 2011.</footnote>
        <footnote id="F2">Weighted average sale price for prices ranging from $17.32 to $18.08. 16 shares were sold at $17.39 per share; 22 shares were sold at $17.66 per share; 64 shares were sold at $17.46 per share; 100 shares were sold at each of the following prices: $17.62, $17.70, $17.761, $17.9205, $17.995 and $18.06; 106 shares were sold at $17.61 per share; 150 shares were sold at $17.785 per share; 200 shares were sold at $17.735 per share; 268 shares were sold at $17.34 per share; 300 shares were sold at each of the following prices: $17.54, $17.645, $17.74, $17.815, $17.94, $18.02 and $18.08; 400 shares were sold at each of the following prices: $17.63, $17.72, $17.775 and $18.00; 500 shares were sold at each of the following prices: $17.71, $17.825, $17.83, $17.89, $17.895 and $17.97; 600 shares were sold at $18.05 per share; 658 shares were sold at $17.82 per share; 700 shares were sold at each of the following prices: $17.50, $17.84 and $17.98 (continued in footnote 3).</footnote>
        <footnote id="F3">(Continued from footnote 2) 800 shares were sold at each of the following prices: $17.32, $17.40, $17.51, $17.87 and $17.96; 889 shares were sold at $17.86 per share; 900 shares were sold at each of the following prices: $17.41 and $17.90; 1,000 shares were sold at each of the following prices: $17.36, $17.73 and $17.95; 1,053 shares were sold at $17.91 per share; 1,096 shares were sold at $17.38 per share; 1,100 shares were sold at $17.64 per share; 1,140 shares were sold at $17.85 per share; 1,200 shares were sold at $17.58 per share; 1,234 shares were sold at $17.68 per share; 1,300 shares were sold at $18.01 per share; 1,460 shares were sold at $17.88 per share; 1,500 shares were sold at $18.03 per share; 1,740 shares were sold at $17.99 per share; 1,800 shares were sold at $17.56 per share; 1,900 shares were sold at $17.43 per share; 1,978 shares were sold at $17.65 per share (continued in footnote 4).</footnote>
        <footnote id="F4">(Continued from footnote 3) 2,000 shares were sold at each of the following prices: $17.44, $17.69, $17.81 and $17.92; 2,100 shares were sold at $17.53 per share; 2,166 shares were sold at $17.67 per share; 2,251 shares were sold at $17.42 per share; 2,336 shares were sold at $17.45 per share; 2,441 shares were sold at $17.33 per share; 2,500 shares were sold at $17.55 per share; 2,659 shares were sold at $17.78 per share; 2,860 shares were sold at $17.93 per share; 3,094 shares were sold at $17.60 per share; 3,191 shares were sold at $17.79 per share; 3,600 shares were sold $17.80 per share; 3,879 shares were sold at $17.37 per share; 4,700 shares were sold at $17.75 per share; 4,800 shares were sold at $17.77 per share; 4,900 shares were sold at $17.76 per share; and 5,900 shares were sold at $17.57 per share.</footnote>
        <footnote id="F5">Weighted average sales price for prices ranging from $17.22 to $17.46.  100 shares were sold at each of the following prices: $17.22, $17.305, $17.31, $17.361 and $17.401; 200 shares were sold at $17.34 per share; 300 shares were sold at each of the following prices: $17.28, $17.30, $17.3004, $17.42, $17.44 and $17.46; 302 shares were sold at $17.33 per share; 400 shares were sold at each of the following prices: $17.29 and $17.315; 600 shares were sold at each of the following prices: $17.24, $17.39 and $17.40; 900 shares were sold at $17.41 per share; 1,600 shares were sold at $17.36 per share; 2,200 shares were sold at $17.35 per share; 2,298 shares were sold at $17.38 per share; and 4,600 shares were sold at $17.37 per share.</footnote>
        <footnote id="F6">The option was granted on October 18, 2006 and became exercisable one quarter on each anniversary of the grant date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ E. Livingston B. Haskell, Power of Attorney for Jeffrey W. Griffiths</signatureName>
        <signatureDate>2012-01-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
