<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><Version>2.4.0.8</Version><ReportLongName>1080 - Disclosure - Stockholder's Equity</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><CurrencyCode /><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName /><CurrencySymbol /><contextRef><ContextID>D2013Q2YTD</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0000946840</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-06-30T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="6 Months Ended" /><Label Key="Calendar" Id="1" Label="Jun. 30, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>1</Level><ElementName>us-gaap_StockholdersEquityNoteAbstract</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Stockholder's Equity</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_StockholdersEquityNoteDisclosureTextBlock</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>terseLabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="D2013Q2YTD" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;div style="font-size:10.0pt;font-family:Times New Roman;"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;b&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt; FONT-WEIGHT: bold;" size="2"&gt;Note 8. Stockholder&amp;#8217;s Equity&lt;/font&gt;&lt;/b&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;i&gt;&lt;font style="FONT-STYLE: italic; FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Preferred Stock&lt;/font&gt;&lt;/i&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;The Company&amp;#8217;s Board of Directors has the authority, without action by the holders of common stock, to issue up to 5,000,000 shares of preferred stock from time to time in such series and with such preference and rights as it may designate.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;i&gt;&lt;font style="FONT-STYLE: italic; FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Share Repurchase Program&lt;/font&gt;&lt;/i&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;On March&amp;#160;9, 2011, our Board of Directors authorized the use of up to $150 million to repurchase shares of our common stock and/or our 2% Senior Convertible Notes due 2017. On September&amp;#160;14, 2011, our Board of Directors authorized the use of up to an additional $200 million to repurchase shares of our common stock and/or our 2% Senior Convertible Notes due 2017. On September&amp;#160;7, 2012, our Board of Directors authorized the use of up to an additional $200 million to repurchase shares of our common stock and/or our 2% Senior Convertible Notes due 2017. Purchases may be made by means of open market transactions, block transactions, privately negotiated purchase transactions or other techniques from time to time.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;During 2012, through open market purchases, we reacquired approximately 6.9 million shares at a cost of approximately $180.3 million or an average price of $26.20 per share and during 2011, we reacquired approximately 9.2 million shares at a cost of approximately $169.7 million or an average price of $18.52 per share.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;At June&amp;#160;30, 2013 we have approximately $200.0 million available under these authorizations to repurchase shares of our common stock and/or our 2% Senior Convertible Notes due 2017. However, our ability to repurchase shares is currently limited by certain terms of our&lt;/font&gt; &lt;font style="FONT-SIZE: 10pt;" size="2"&gt;Credit Agreement.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;i&gt;&lt;font style="FONT-STYLE: italic; FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Senior convertible notes&lt;/font&gt;&lt;/i&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Our senior convertible notes were convertible into shares of our common stock during the second quarter of 2013 at the election of the holders as the last reported sale price of our common stock for the 20 or more trading days in the 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeded 130% of the conversion price, $18.87 per share. During the quarter note holders converted notes with a face value of $12 thousand and we issued the holders 634 shares of our common stock.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Our senior convertible notes continue to be convertible into shares of our common stock during the third quarter of 2013.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;/div&gt;</NonNumbericText><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>nonnum:textBlockItemType</ElementDataType><SimpleDataType>na</SimpleDataType><ElementDefenition>The entire disclosure for shareholders' equity, comprised of portions attributable to the parent entity and noncontrolling interest, if any, including other comprehensive income (as applicable).  Including, but not limited to: (1) balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings; (2) accumulated balance for each classification of other comprehensive income and total amount of comprehensive income; (3) amount and nature of changes in separate accounts, including the number of shares authorized and outstanding, number of shares issued upon exercise and conversion, and for other comprehensive income, the adjustments for reclassifications to net income; (4) rights and privileges of each class of stock authorized; (5) basis of treasury stock, if other than cost, and amounts paid and accounting treatment for treasury stock purchased significantly in excess of market; (6) dividends paid or payable per share and in the aggregate for each class of stock for each period presented; (7) dividend restrictions and accumulated preferred dividends in arrears (in aggregate and per share amount); (8) retained earnings appropriations or restrictions, such as dividend restrictions; (9) impact of change in accounting principle, initial adoption of new accounting principle and correction of an error in previously issued financial statements; (10) shares held in trust for Employee Stock Ownership Plan (ESOP); (11) deferred compensation related to issuance of capital stock; (12) note received for issuance of stock; (13) unamortized discount on shares; (14) description, terms, and number of warrants or rights outstanding; (15) shares under subscription and subscription receivables, effective date of new retained earnings after quasi-reorganization and deficit eliminated by quasi-reorganization and, for a period of at least ten years after the effective date, the point in time from which the new retained dates; and (16) retroactive effective of subsequent change in capital structure.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 08

 -Article 4



Reference 2: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 30

 -Section 50

 -Paragraph 2

 -URI http://asc.fasb.org/extlink&amp;oid=6405834&amp;loc=d3e23285-112656



Reference 3: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 02

 -Paragraph 29, 30, 31

 -Article 5



Reference 4: http://www.xbrl.org/2003/role/presentationRef

 -Publisher AICPA

 -Name Accounting Research Bulletin (ARB)

 -Number 43

 -Section B

 -Paragraph 7, 11A

 -Chapter 1

 -LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009.  This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.



Reference 5: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 6

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21506-112644



Reference 6: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Statement of Financial Accounting Standard (FAS)

 -Number 5

 -Paragraph 15

 -LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009.  This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.



Reference 7: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 310

 -SubTopic 10

 -Section S99

 -Paragraph 2

 -Subparagraph (SAB TOPIC 4.E)

 -URI http://asc.fasb.org/extlink&amp;oid=6228006&amp;loc=d3e74512-122707



Reference 8: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Glossary Preferred Stock

 -URI http://asc.fasb.org/extlink&amp;oid=6521494



Reference 9: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section S99

 -Paragraph 4

 -Subparagraph (SAB TOPIC 4.C)

 -URI http://asc.fasb.org/extlink&amp;oid=6959260&amp;loc=d3e187143-122770



Reference 10: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 235

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.4-08.(d),(e))

 -URI http://asc.fasb.org/extlink&amp;oid=6881521&amp;loc=d3e23780-122690



Reference 11: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Statement of Financial Accounting Standard (FAS)

 -Number 129

 -Paragraph 2, 3, 4, 5, 6, 7, 8

 -LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009.  This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.



Reference 12: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Staff Accounting Bulletin (SAB)

 -Number Topic 4

 -Section C



Reference 13: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Staff Accounting Bulletin (SAB)

 -Number Topic 4

 -Section E



Reference 14: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 210

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.5-02.29-31)

 -URI http://asc.fasb.org/extlink&amp;oid=6877327&amp;loc=d3e13212-122682



Reference 15: http://www.xbrl.org/2003/role/presentationRef

 -Publisher AICPA

 -Name Accounting Principles Board Opinion (APB)

 -Number 12

 -Paragraph 10

 -LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009.  This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.



Reference 16: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 04

 -Article 3



Reference 17: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 2

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21463-112644



Reference 18: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.3-04)

 -URI http://asc.fasb.org/extlink&amp;oid=6959260&amp;loc=d3e187085-122770



Reference 19: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 11

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21564-112644



Reference 20: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21475-112644



Reference 21: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 4

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21484-112644



Reference 22: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 5

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21488-112644



Reference 23: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 08

 -Paragraph d

 -Article 4



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Stockholder's Equity</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Stockholder's Equity</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Sheet</ReportType><RoleURI>http://www.viropharma.com/role/DisclosureStockholdersEquity</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
