AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS RIGHTS AGREEMENT

Exhibit 4.4

AMENDMENT NO. 2 TO

AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT

This Amendment No. 2 (the “Amendment”) to the Amended and Restated Investors’ Rights Agreement, dated as of December 22, 2005, as amended on December 28, 2009 (the “Agreement”), is made and entered into by and among WageWorks, Inc., a Delaware corporation (the “Company”), and the undersigned parties to the Agreement as of the 30th day of July, 2010. Capitalized terms used herein and not defined herein shall have the meanings set forth in the Agreement.

WHEREAS, the Company, the Holders and the Founders have previously entered into the Agreement and Amendment No. 1 to the Agreement;

WHEREAS, the Company has entered into a Note and Warrant Purchase Agreement, dated as of December 28, 2009 (the “Purchase Agreement”), with certain of the Holders, pursuant to which the Company has agreed to sell to such Holders convertible promissory notes and, in certain circumstances, related warrants to acquire shares of the Company’s capital stock;

WHEREAS, pursuant to the terms of the Purchase Agreement, the Company issued certain Convertible Promissory Notes (the “Notes”) and certain Warrants to Purchase Shares of Preferred Stock (the “Original Warrants”) to the Investors (as such term is defined in the Purchase Agreement).

WHEREAS, the Company and the Investors desire to amend the Purchase Agreement to provide for the creation of a new series of Series E-1 Preferred Stock, $0.001 par value, and to exchange the Original Warrants for Amended and Restated Warrants to Purchase Shares of Preferred Stock that are exercisable for shares of the Company’s Series E-1 Preferred Stock (and not for shares of the Company’s Series E Preferred Stock); and

WHEREAS, pursuant to Section 3.7 of the Agreement, the Agreement may be amended by a written amendment executed by the Company and the holders (other than Founders) of more than 50% in interest of the Registrable Securities held by the Holders.

NOW, THEREFORE, in consideration of the foregoing and for good and valid consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound hereby, the parties agree as follows:

1. Clause (vii) of Section 1.1(f) of the Agreement is hereby deleted and replaced in its entirety by the following:

“(vii) the Common Stock issuable or issued upon conversion of any series of the Company’s preferred stock issued or issuable upon conversion of the notes and exercise of the warrants issued under that certain Note and Wan-ant Purchase Agreement, dated as of December 28, 2009, as may be amended from time to time (the “Note and Warrant Purchase Agreement”), among the Company and certain of the Holders,”

2. This Amendment shall be binding upon and inure to the benefit of the parties hereto and their respective successors and permitted assigns, shall be governed by and construed in accordance with the laws of the State of Delaware and may not be modified or amended except by a written agreement signed by both of the parties hereto.

3. This Amendment may be executed in one or more counterparts (including by facsimile), each of which shall be deemed to be an original, but all of which taken together shall constitute one and the same instrument.

4. Except as specifically amended by this Amendment, the Agreement shall remain in full force and effect.

[The remainder of this page has been intentionally left blank.]

-2-

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

The parties have caused this Amendment to be duly executed and delivered by their proper and duly authorized representatives as of the date and year first written above.

[AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]