﻿<?xml version="1.0" encoding="utf-8"?>
<InstanceReport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <Version>2.2.0.7</Version>
  <hasSegments>false</hasSegments>
  <ReportName>Employee Stock-Based Compensation</ReportName>
  <ReportLongName>0219 - Disclosure - Employee Stock-Based Compensation</ReportLongName>
  <DisplayLabelColumn>true</DisplayLabelColumn>
  <ShowElementNames>false</ShowElementNames>
  <RoundingOption />
  <HasEmbeddedReports>false</HasEmbeddedReports>
  <Columns>
    <Column>
      <LabelColumn>false</LabelColumn>
      <Id>1</Id>
      <Labels>
        <Label Id="1" Label="9 Months Ended" />
        <Label Id="2" Label="Sep. 24, 2010" />
      </Labels>
      <CurrencyCode>USD</CurrencyCode>
      <FootnoteIndexer />
      <hasSegments>false</hasSegments>
      <hasScenarios>false</hasScenarios>
      <Segments />
      <Scenarios />
      <Units>
        <Unit>
          <UnitID>USD</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>Shares</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>Pure</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>pure</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>USDEPS</UnitID>
          <UnitType>Divide</UnitType>
          <NumeratorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </NumeratorMeasure>
          <DenominatorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </DenominatorMeasure>
          <Scale>0</Scale>
        </Unit>
      </Units>
      <CurrencySymbol>$</CurrencySymbol>
    </Column>
  </Columns>
  <Rows>
    <Row>
      <Id>2</Id>
      <Label>Employee Stock-Based Compensation [Abstract]</Label>
      <Level>0</Level>
      <ElementName>us-gaap_ShareBasedCompensationAbstract</ElementName>
      <ElementPrefix>us-gaap</ElementPrefix>
      <IsBaseElement>true</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>No definition available.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>true</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole />
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText />
          <NonNumericTextHeader />
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>xbrli:stringItemType</ElementDataType>
      <SimpleDataType>string</SimpleDataType>
      <ElementDefenition>No definition available.</ElementDefenition>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
    <Row>
      <Id>3</Id>
      <Label>Employee Stock-Based Compensation</Label>
      <Level>1</Level>
      <ElementName>us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock</ElementName>
      <ElementPrefix>us-gaap</ElementPrefix>
      <IsBaseElement>true</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>No definition available.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>false</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole>verboselabel</PreferredLabelRole>
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note 19 - us-gaap:DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock--&gt;
   &lt;div style="margin-left: 0%"&gt;
   &lt;div style="margin-top: 12pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;table width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt; font-family: Arial, Helvetica; color: #000000; background: transparent; text-align: left"&gt;
   &lt;tr&gt;
       &lt;td width="2%"&gt;&lt;/td&gt;
       &lt;td width="98%"&gt;&lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr valign="top"&gt;
       &lt;td&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;19.&amp;#160;&lt;/font&gt;&lt;/b&gt;
   &lt;/td&gt;
       &lt;td&gt;
       &lt;b&gt;&lt;font style="font-family: 'Times New Roman', Times"&gt;Employee
       Stock-Based Compensation&lt;/font&gt;&lt;/b&gt;
   &lt;/td&gt;
   &lt;/tr&gt;
   &lt;/table&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 2%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       During the
       &lt;font style="white-space: nowrap"&gt;year-to-date&lt;/font&gt;
       period ended September&amp;#160;24, 2010, the Company granted
       stock-based compensation awards under the 2008 Long Term
       Performance Plan (2008 LTPP) in the form of stock options,
       restricted stock units and performance units.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 2%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       &lt;i&gt;Stock Options.&lt;/i&gt; The Company granted 555,363 stock options
       with an exercise price equal to the fair market value of L-3
       Holdings&amp;#8217; common stock on the date of grant. The options
       expire after 10&amp;#160;years from the date of grant and vest
       ratably over a three-year period on the annual anniversary of
       the date of grant. The weighted average grant date fair value
       for the options awarded was $18.41 and was
   estimated using the Black-Scholes option-pricing model. The
       weighted average assumptions used in the valuation model for
       options granted during the
       &lt;font style="white-space: nowrap"&gt;year-to-date&lt;/font&gt;
       period ended September&amp;#160;24, 2010 are presented in the table
       below:
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;table border="0" width="100%" align="center" cellpadding="0" cellspacing="0" style="font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent; text-align: left"&gt;
   &lt;!-- Table Width Row BEGIN --&gt;
   &lt;tr style="font-size: 1pt" valign="bottom"&gt;
       &lt;td width="95%"&gt;&amp;#160;&lt;/td&gt;&lt;!-- colindex=01 type=maindata --&gt;
       &lt;td width="2%"&gt;&amp;#160;&lt;/td&gt;&lt;!-- colindex=02 type=gutter --&gt;
       &lt;td width="1%" align="right"&gt;&amp;#160;&lt;/td&gt;&lt;!-- colindex=02 type=lead --&gt;
       &lt;td width="1%" align="right"&gt;&amp;#160;&lt;/td&gt;&lt;!-- colindex=02 type=body --&gt;
       &lt;td width="1%" align="left"&gt;&amp;#160;&lt;/td&gt;&lt;!-- colindex=02 type=hang1 --&gt;
   &lt;/tr&gt;
   &lt;!-- Table Width Row END --&gt;
   &lt;!-- TableOutputHead --&gt;
   &lt;!-- TableOutputBody --&gt;
   &lt;tr valign="bottom" style="background: #cceeff"&gt;
   &lt;td align="left" valign="bottom"&gt;
   &lt;div style="text-indent: -10pt; margin-left: 10pt"&gt;
       Expected holding period (in years)
   &lt;/div&gt;
   &lt;/td&gt;
   &lt;td&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
       4.7
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="left" valign="bottom"&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr valign="bottom"&gt;
   &lt;td nowrap="nowrap" align="left" valign="bottom"&gt;
   &lt;div style="text-indent: -10pt; margin-left: 10pt"&gt;
       Expected volatility
   &lt;/div&gt;
   &lt;/td&gt;
   &lt;td&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
       26.2
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="left" valign="bottom"&gt;
       %
   &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr valign="bottom" style="background: #cceeff"&gt;
   &lt;td align="left" valign="bottom"&gt;
   &lt;div style="text-indent: -10pt; margin-left: 10pt"&gt;
       Expected dividend yield
   &lt;/div&gt;
   &lt;/td&gt;
   &lt;td&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
       2.2
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="left" valign="bottom"&gt;
       %
   &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr valign="bottom"&gt;
   &lt;td align="left" valign="bottom"&gt;
   &lt;div style="text-indent: -10pt; margin-left: 10pt"&gt;
       Risk-free interest rate
   &lt;/div&gt;
   &lt;/td&gt;
   &lt;td&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
   &amp;#160;
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="right" valign="bottom"&gt;
       2.3
   &lt;/td&gt;
   &lt;td nowrap="nowrap" align="left" valign="bottom"&gt;
       %
   &lt;/td&gt;
   &lt;/tr&gt;
   &lt;/table&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 0%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 2%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       &lt;i&gt;Restricted Stock Units.&lt;/i&gt; The Company granted 603,020
       restricted stock units with a weighted average grant date fair
       value of $90.24 per share. These units automatically convert
       into shares of L-3 Holdings&amp;#8217; common stock upon vesting, and
       are subject to forfeiture until certain restrictions have
       lapsed, including a three year cliff vesting period for
       employees and a one year cliff vesting period for non-employee
       directors, in each case starting on the date of grant.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 2%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       &lt;i&gt;Performance Units.&lt;/i&gt; The Company granted 69,918 performance
       units with a weighted average grant date fair value per unit of
       $103.71. The payout for these units is based on the achievement
       of pre-determined performance goals established by the
       compensation committee of the Company&amp;#8217;s Board of Directors
       for the three-year period ending December&amp;#160;31, 2012. The
       payout can range from zero to 200% of the original number of
       units awarded, which are converted into shares of L-3
       Holdings&amp;#8217; common stock
       &lt;font style="white-space: nowrap"&gt;and/or&lt;/font&gt; an
       amount of cash based on the then existing closing price at the
       end of the performance period.
   &lt;/div&gt;
   &lt;div style="margin-top: 6pt; font-size: 1pt"&gt;&amp;#160;
   &lt;/div&gt;
   &lt;div align="left" style="margin-left: 0%; margin-right: 0%; text-indent: 2%; font-size: 10pt; font-family: 'Times New Roman', Times; color: #000000; background: transparent"&gt;
       On April&amp;#160;27, 2010, the stockholders of L-3 Holdings
       approved an amendment to the 2008 LTPP. The principal purpose of
       the amendment was to increase the number of shares authorized
       for issuance under the 2008 LTPP to approximately
       12.2&amp;#160;million shares, except that each share of L-3
       Holdings&amp;#8217; common stock issued under a &amp;#8220;full
       value&amp;#8221; award (awards other than stock options or stock
       appreciation rights) will be counted as 2.6&amp;#160;shares for
       purposes of this share limit.
   &lt;/div&gt;
   &lt;/div&gt;
</NonNumbericText>
          <NonNumericTextHeader>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note</NonNumericTextHeader>
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>us-types:textBlockItemType</ElementDataType>
      <SimpleDataType>textblock</SimpleDataType>
      <ElementDefenition>Disclosure of compensation-related costs for share-based compensation which may include disclosure of policies, compensation plan details, allocation of stock compensation, incentive distributions, share-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.</ElementDefenition>
      <ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name Statement of Financial Accounting Standard (FAS)
 -Number 123R
 -Paragraph 64, 65, A240

Reference 2: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Statement of Position (SOP)
 -Number 93-6
 -Paragraph 53

Reference 3: http://www.xbrl.org/2003/role/presentationRef
 -Publisher SEC
 -Name Staff Accounting Bulletin (SAB)
 -Number Topic 14

</ElementReferences>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
  </Rows>
  <Footnotes />
  <NumberOfCols>1</NumberOfCols>
  <NumberOfRows>2</NumberOfRows>
  <HasScenarios>false</HasScenarios>
  <MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel>
  <SharesRoundingLevel>UnKnown</SharesRoundingLevel>
  <PerShareRoundingLevel>UnKnown</PerShareRoundingLevel>
  <HasPureData>false</HasPureData>
  <SharesShouldBeRounded>true</SharesShouldBeRounded>
</InstanceReport>
