ALLSCRIPTS HEALTHCARE SOLUTIONS, INC. Performance-Based RestrictedStock Unit Award Agreement Performance-Based Vesting Relative TSR

Exhibit 10.39

ALLSCRIPTS HEALTHCARE SOLUTIONS, INC.

Performance-Based Restricted Stock Unit Award Agreement

Performance-Based Vesting – Relative TSR

THIS AGREEMENT is made as of [            ] (the “Grant Date”), by and between Allscripts Healthcare Solutions, Inc., a Delaware corporation (“Company”), and [            ] (the “Participant”).

WHEREAS, the Participant is expected to perform valuable services for the Company and the Company considers it desirable and in its best interests that the Participant be given a proprietary interest in the Company and an incentive to advance the interests of the Company by possessing units that are settled in shares of the Company’s Common Stock, $.01 par value per share (the “Common Stock”), in accordance with the Company’s 2011 Stock Incentive Plan (the “Plan”).

NOW THEREFORE, in consideration of the foregoing premises, it is agreed by and between the parties as follows:

Cause. “Cause” shall mean (i) the willful or grossly negligent failure by the Participant to perform his or her duties and obligations in any material respect, other than any such failure resulting from the disability of the Participant, (ii) the Participant’s conviction of a crime or offense involving the property of the Company, or any crime or offense constituting a felony or involving fraud or moral turpitude; (iii) the Participant’s violation of any law, which violation is materially and demonstrably injurious to the operations or reputation of the Company; or (iv) the Participant’s material violation of any generally recognized policy of the Company; provided, however, that if the term “Cause” is defined in an employment agreement between the Company and the Participant, the definition in the employment agreement shall apply for purpose of this Agreement.

Good Reason. “Good Reason” shall mean (i) any significant diminution in the Participant’s responsibilities from and after the date of the Change in Control, (ii) any material reduction in the annual salary or target incentive cash compensation of the Participant from and after the date of the Change in Control or (iii) any requirement after the date of the Change in Control (or prior thereto in connection with the Change in Control) to relocate to a location that is more than

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fifty (50) miles from the principal work location of the Participant; provided, however, that the occurrence of any such condition shall not constitute Good Reason unless the Participant provides written notice to the Company of the existence of such condition not later than 90 days after the initial existence of such condition, and the Company shall have failed to remedy such condition within 30 days after receipt of such notice.

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In the event that there is any change in the number of issued shares of Common Stock of the Company without new consideration to the Company (such as by stock dividends or stock split-ups), then the number of unvested performance-based restricted stock units subject to this Performance-Based Restricted Stock Unit Award shall be adjusted in proportion to such change in issued shares.

If the outstanding shares of Common Stock of the Company shall be combined, or be changed into another kind of stock of the Company or into equity securities of another corporation, whether through recapitalization, reorganization, sale, merger, consolidation, etc., the Company shall cause adequate provision to be made whereby the unvested performance-based restricted stock units subject to this Agreement shall be adjusted equitably so that the securities received upon vesting shall be the same as if the vesting had occurred immediately prior to such recapitalization, reorganization, sale, merger, consolidation, etc.

Notwithstanding the foregoing, in the event of a sale of the Company through a merger, consolidation or sale of all or substantially all of its assets where all or part of the consideration is stock, cash or other securities or property (a “Transaction”), the Performance-Based Restricted Stock Unit Award shall be assumed or an award of equivalent value shall be substituted by the successor corporation or a parent or subsidiary of the successor corporation in an economically equivalent manner. In the event that the successor corporation refuses or is unable to assume or substitute for the Performance-Based Restricted Stock Unit Award in an economically equivalent manner, then simultaneously with the consummation of the Transaction, the Participant shall fully vest in the Performance-Based Restricted Stock Unit Award at the level deemed to be earned in accordance with Section 2(b) of this Agreement and such number of performance-based restricted stock units subject to the Performance-Based Restricted Stock Unit Award shall become unrestricted. For the purposes of this Section 5, the Performance-Based Restricted Stock Unit Award shall be considered assumed in an economically equivalent manner only if, following the Transaction, the Performance-Based Restricted Stock Unit Award confers the right to receive, for each performance-based restricted stock unit subject to the Performance-Based Restricted Stock Unit Award and unvested immediately prior to the Transaction, publicly traded shares of common stock of the successor company substantially equal in fair market value to the per share consideration received by holders of shares of Common Stock in the Transaction. The determination of such substantial equality of value of consideration shall be made by the Committee in its sole discretion and its determination shall be conclusive and binding.

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It is intended that any amounts payable under this Performance-Based Restricted Stock Unit Award comply with the provisions of Code Section 409A of the Internal Revenue Code of 1986 and the treasury regulations relating thereto so as not to subject the Participant to the payment of interest and tax penalty which may be imposed under Code Section 409A. In furtherance of this interest, to the extent that any regulations or other

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guidance issued under Code Section 409A after the date of this Performance-Based Restricted Stock Unit Award would result in the Participant being subject to payment of interest and tax penalty under Code Section 409A, the parties agree to amend this Performance-Based Restricted Stock Unit Award in order to bring this Performance-Based Restricted Stock Unit Award into compliance with Code Section 409A. No amount shall be payable pursuant to a termination of the Participant’s employment unless such termination constitutes a separation from service under Section 409A. To the extent any amounts payable upon the Participant’s separation from service are nonqualified deferred compensation under Section 409A, and if the Participant is at such time a specified employee under Section 409A, then to the extent required under Section 409A payment of such amounts shall be postponed until six (6) months following the date of the Participant’s separation from service (or until any earlier date of the Participant death), upon which date all such postponed amounts shall be paid to the Participant in a lump sum, and any remaining payments due shall be paid as otherwise provided herein. The determination of whether the Participant is a specified employee shall made by the Company in accordance with Section 409A.

IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed on the day and year first above written.

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Exhibit A

1. For purposes of this Exhibit:

Following the end of each Performance Period, the Company’s Compensation Committee will certify the level of the Performance Measure achieved by the Company for such Performance Period. The performance-based restricted stock units subject to vesting during a Performance Period will be subject to forfeiture and cancellation by the Company if the Company’s performance during such Performance Period does not meet or exceed the threshold percentile rank of the Performance Measure for such Performance Period. Performance at or above the threshold level will result performance-based restricted stock units becoming vested as set forth below, and shares underlying such vested performance-based restricted stock units shall be distributed following completion of the certification described above.

Notwithstanding the foregoing, following completion of the three-year period commencing on the Grant Date and ending on the third anniversary of the Grant Date (the “Three Year Performance Period”), the Compensation Committee will determine the number of performance-based restricted stock units that would vest if the maximum number of performance-based restricted stock units subject to the Performance-Based Restricted Stock Unit Award had been subject only to the Three Year Performance Period (the “Alternative Three Year Performance Period Vested Unit Calculation”). If the number of performance-based restricted stock units that vest pursuant to the Alternative Three Year Performance Period Vested Unit Calculation is greater than the number of performance-based restricted stock units that vest under this Agreement in the three Performance Periods described herein without regard to the Alternative Three Year Performance Period Vested Unit Calculation, then such greater number of performance-based restricted stock units shall vest pursuant to the Alternative Three Year Performance Period Vested Unit Calculation, reduced by the number of performance-based restricted stock units previously vested. Shares underlying vested performance-based restricted stock units shall be distributed following completion of the certification described above.

2. Additional Definitions.

a. “Comparison Group” means the companies listed on Appendix 1 to this Exhibit A, as may be adjusted as described below.

b. “Performance Period” means each of the following three periods:

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c. “Total Shareholder Return” or “TSR” means total shareholder return as applied to the Company or any company in the Comparison Group, meaning stock price appreciation from the beginning to the end of the Performance Period, plus dividends and distributions made or declared (assuming such dividends or distributions are reinvested in the common stock of the Company or any company in the Comparison Group) during the Performance Period, expressed as a percentage return. Except as modified in Section 4(d), for purposes of computing TSR, the stock price at the beginning of the Performance Period will be the average price of a share of common stock over the 30 trading days ending on the first day of the Performance Period, and the stock price at the end of the Performance Period will be the average price of a share of common stock over the 30 trading days ending on the last day of the Performance Period, adjusted for changes in capital structure; provided, however, that TSR will be negative one hundred percent (-100%) if a company: (i) files for bankruptcy, reorganization, or liquidation under any chapter of the U.S. Bankruptcy Code; (ii) is the subject of an involuntary bankruptcy proceeding that is not dismissed within 30 days; (iii) is the subject of a stockholder approved plan of liquidation or dissolution; or (iv) ceases to conduct substantial business operations.

3. Calculation. For purposes of the award, the number of shares earned will be calculated as follows:

FIRST: For the Company and for each other company in the Comparison Group, determine the TSR for the Performance Period.

SECOND: Rank the TSR values determined in the first step from low to high (with the company having the lowest TSR being ranked number 1, the company with the second lowest TSR ranked number 2, and so on) and determine the Company’s percentile rank based upon its position in the list by dividing the Company’s position by the total number of companies (including the Company) in the Comparison Group and rounding the quotient to the nearest hundredth. For example, if the Company were ranked 60 on the list out of 80 companies (including the Company), its percentile rank would be 75%.

THIRD: Plot the percentile rank for the Company determined in the second step into the appropriate band in the left-hand column of the table below and determine the number of shares earned as a percent of target, which is the figure in the right-hand column of the table below corresponding to that percentile rank. Use linear interpolation between points in the table below to determine the percentile rank and the corresponding share funding if the Company’s percentile rank is greater than     % and less than     % but not exactly one of the percentile ranks listed in the left-hand column. For example, if the Company’s percentile rank is     %, then     % of target shares would be earned.

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4. Rules. The following rules apply to the computation of the number of shares earned:

a. If the Company’s absolute TSR is negative over any of the three Performance Periods, payouts shall not exceed 100% of target for that Performance Period. The aggregate value of the shares earned and settled in each Performance Period, based on the Fair Market Value of such shares as of the date of settlement, shall not exceed five (5) times the target payment value for such performance period.

b. The minimum earnout is zero and the maximum earnout is 200% of target. There is no minimum number of shares or other consideration that recipient will receive, and no shares will be earned if the percentile rank is          percentile or lower in a Performance Period.

c. For purposes of computing Total Shareholder Return for the Company and each other company in the Comparison Group, the stock price at the beginning and end of the Performance Period will, subject to Section 2 of the Performance-Based Restricted Stock Unit Award Agreement, be determined as the 30-day average closing price of the stock on each of the 30 consecutive trading days ending on and including the first day or last day of the Performance Period, as the case may be.

d. Companies shall be removed from the Comparison Group if they undergo a Specified Corporate Change. A company that is removed from the Comparison Group before the measurement date will not be included at all in the computation of the performance factor. A company in the Comparison Group will be deemed to have undergone a “Specified Corporate Change” if it:

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The Company shall rely on press releases, public filings, website postings, and other reasonably reliable information available regarding a peer company in making a determination that a Specified Corporate Change has occurred.

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Appendix 1 to

Exhibit A to

Performance-Based Stock Unit Agreement

Comparison Group