Exhibit 10.1

AMENDMENT NO. 2 TO THE THIRD AMENDED AND RESTATED

INVESTORS’ RIGHTS AGREEMENT

This AMENDMENT NO. 2 TO THE THIRD AMENDED AND RESTATED INVESTORS’ RIGHTS
AGREEMENT is dated as of August 5, 2010 (this “Amendment”) and is entered into
by and among NeurogesX, Inc., a Delaware corporation (the “Company”), the
parties defined as “Investors” in the IRA (as defined below) (each a “Prior
Investor,” and collectively, the “Prior Investors”). The Third Amended and
Restated Investors’ Rights Agreement dated as of November 14, 2005, as amended,
shall be hereinafter referred to as the “IRA.”

RECITALS

WHEREAS, the Company and the undersigned Prior Investors (on behalf of all Prior
Investors) desire to amend Section 1.14 of the IRA; and

WHEREAS, Section 4.3 of the IRA allows the amendment of the IRA with the written
consent of the Company and the holders of at least a majority of the Registrable
Securities, as defined in the IRA, outstanding.

WHEREAS, the undersigned Prior Investors hold sufficient shares of Registrable
Securities to amend the IRA pursuant to Section 4.3 thereto.

NOW, THEREFORE, in consideration of the promises contained herein and for other
good and valuable consideration, the receipt and sufficiency of which is hereby
mutually acknowledged by the parties hereto, the parties hereby covenant and
agree as follows:

1. Amendment to Section 1.14. Section 1.14 of the IRA is hereby amended and
restated to read in its entirety as follows:

“1.14 Termination/Deferral of Registration Rights. The right of any Holder to
request registration or inclusion in any registration pursuant to Section 1.2,
1.3 or 1.5 shall terminate on June 30, 2013. Prior to such termination, a Holder
of Registrable Securities consisting of less than 1% of the then outstanding
shares of capital stock of the Company shall not have registration rights under
Sections 1.2 or 1.5 hereof during any period of time prior to such termination
when all Registrable Securities held (or deemed held) by such Holder may be sold
pursuant to Rule 144 under the Securities Act (or any successor regulation)
during a three month period. For purposes of this Agreement the term “Qualified
IPO” shall mean the initial public offering of Common Stock of the Company which
occurred on May 1, 2007.”

2. Except as set forth in this Amendment, the provisions of the IRA shall remain
unchanged and shall continue in full force and effect.

[Signature Pages Follow]

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IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the
date first written above.

 

NEUROGESX, INC. By:   /s/ Anthony DiTonno   Anthony DiTonno   President and
Chief Executive Officer

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]

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PRIOR INVESTOR:     ARCH Venture Fund V, L.P.     By:   ARCH Venture Partners V,
L.P.     Its:   General Partner     By:   ARCH Venture Partners V, LLC     Its:
  General Partner     By:  

/s/ Robert T. Nelsen

    Its:   Managing Director     ARCH V Entrepreneurs Fund, L.P.     By:   ARCH
Venture Partners V, L.P.     Its:   General Partner     By:   ARCH Venture
Partners V, LLC     Its:   General Partner     By:  

/s/ Robert T. Nelsen

    Its:   Managing Director     Healthcare Focus Fund, L.P.     By:   ARCH
Venture Partners V, L.P.     Its:   General Partner     By:   ARCH Venture
Partners V, LLC     Its:   General Partner     By:  

/s/ Robert T. Nelsen

    Its:   Managing Director

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]

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PRIOR INVESTOR:     Montreux Equity Partners II SBIC, L.P.     By:   Montreux
Equity Management II SBIC,       LLC, its General Partner     By:  

/s/ Daniel K. Turner III

    Name:   Daniel K. Turner III     Title:   Managing Member     Montreux
Equity Partners III SBIC, L.P.     By:   Montreux Equity Management III SBIC,  
    LLC, its General Partner     By:  

/s/ Daniel K. Turner III

    Name:   Daniel K. Turner III     Title:   Managing Member

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]

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PRIOR INVESTOR:     Pacven Walden Ventures V, L.P.     By:   Pacven Walden
Management V, Co., Ltd.     Its:   General Partner     By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, Director     Pacven Walden Ventures Parallel V-A C.V.     By:
  Pacven Walden Management V, Co., Ltd.     Its:   General Partner     By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, Director     Pacven Walden Ventures Parallel V-B C.V.     By:
  Pacven Walden Management V, Co., Ltd.     Its:   General Partner     By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, Director     Pacven Walden Ventures V-QP Associates Fund, L.P.
    By:   Pacven Walden Management V, Co., Ltd.     Its:   General Partner    
By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, Director     Seed Ventures III Pte. Ltd.     By:  

/s/ Loo Hock Voon

      Loo Hock Voon, Liquidator

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]

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PRIOR INVESTOR:     International Venture Capital Investment III Corporation    
By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, President     International Venture Capital Investment
Corporation     By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, President     Asian Venture Capital Investment Corporation    
By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan, President     Pacven Walden Ventures V Associates Fund, L.P.  
  By:  

/s/ Lip-Bu Tan

      Lip-Bu Tan

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]

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PRIOR INVESTOR:     The Global Life Sciences Ventures Funds II GmbH & Co. KG    

Represented by its General Partner

The Global Life Sciences Ventures GmbH

    By:  

/s/ Hanns-Peter Wiese

    Title:  

Hanns-Peter Wiese, Partner

    The Global Life Sciences Ventures Funds II Limited Partnership    
Represented by its General Partner     Global Life Sciences Ventures (GP)
Limited     By:  

/s/ Connie Helyor

    Title:  

Connie Helyor, Director

[Signature Page to Amendment No. 2 to the NeurogesX Third Amended and Restated
Investors’ Rights Agreement]