AMENDMENT AND WAIVER TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

Exhibit 4.3

AMENDMENT AND WAIVER

TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

This Amendment and Waiver to Amended and Restated Investor Rights Agreement (the “Amendment”) is made and entered into effective March 31, 2010 by and among Ellie Mae, Inc., a Delaware corporation (the “Company”), and the persons holding the majority of the outstanding Registrable Securities and set forth on the signature pages hereto (the “Majority Holders”).

RECITALS

WHEREAS, the Company’s predecessor, Ellie Mae, Inc., a California corporation (the “Predecessor”), and the Majority Holders are party to that Amended and Restated Investor Rights Agreement, dated December 21, 2005 (the “Investor Rights Agreement”) (capitalized terms used but not defined herein have the meaning ascribed to them in the Agreement);

WHEREAS, the Company became party to the Investor Rights Agreement by operation of law upon the reincorporation of the Predecessor as the Company effective November 30, 2009;

WHEREAS, under Section 6.2 of the Investor Rights Agreement, the Company and Holders of at least a majority of the Registrable Securities (as such term is defined in the Investor Rights Agreement) may amend, on behalf of all other holders of Registrable Securities, terms of the Investor Rights Agreement;

WHEREAS, the Majority Holders hold at least a majority of the Registrable Securities; and

WHEREAS, the Majority Holders and the Company now desire to amend the Investor Rights Agreement.

AGREEMENT

NOW, THEREFORE, in consideration of the foregoing, the parties hereto agree as follows:

3.1 “New Securities”. For purposes of this Section 3, the term “New Securities” shall mean shares of Common Stock, Preferred Stock or any other class of capital stock of the Company, whether or not now authorized, securities of any type that are convertible into shares of such capital stock, and options, warrants or rights to acquire shares of such capital stock. Notwithstanding the foregoing, the term “New Securities” shall not include: (a) securities issuable upon conversion of the Series A Preferred Stock, Series B Preferred Stock, Series C Preferred Stock, Series D Preferred Stock, Series E Preferred Stock, Series F Preferred Stock, Series G Preferred Stock, Series G-2 Preferred Stock or Series H Preferred Stock; (b) securities offered to the public pursuant to a registration statement filed under the Securities Act; (c) securities issued pursuant to the acquisition of another corporation by the Company by merger, purchase of substantially all of the assets, or other reorganization whereby the Company owns not less than 51% of the voting power of such corporation; (d) up to an aggregate of 12,250,000 shares of Common Stock (or related options) issued or issuable at any time to officers, directors,

employees or consultants of the Company, pursuant to any stock grant, stock option plan or stock purchase plan or other stock incentive agreement or arrangement approved by the Board of Directors (which figure shall include any options outstanding on the date hereof); (e) securities issued in connection with equipment lease or working capital debt financings, so long as the number of securities so issued does not exceed one percent of the then outstanding capital stock of the Company; (f) convertible securities issued in connection with business or partnership relationships with third parties designed to incentivize such third parties; (g) shares of Common Stock or Preferred Stock issued in connection with any stock split, stock dividend or recapitalization of the Company; and (h) shares of the Company’s capital stock issued pursuant to Exchange Agreements (as such term is defined in the Company’s Amended and Restated Certificate of Incorporation).

[SIGNATURE PAGES FOLLOW]

2

The parties have executed this Amendment as of the date first set forth above.

Signature Page to Amendment to Amended and Restated Investor Rights Agreement

MAJORITY STOCKHOLDERS:

Signature Page to Amendment to Amended and Restated Investor Rights Agreement

Signature Page to Amendment to Amended and Restated Investor Rights Agreement

Signature Page to Amendment to Amended and Restated Investor Rights Agreement

Signature Page to Amendment to Amended and Restated Investor Rights Agreement