EXHIBIT 23.1 CONSENT OF INDEPENDENT ACCOUNTANTS We hereby consent to the incorporation by reference in the Registration Statements on Forms S-8 (File Nos. 333-106035, 333-105299, 333-105298, 333-105297, 333-68058, 333-55705, 333-43046, 333-43044, 333-25369, 333-25371, and 333-25369) and Form S-3 (File Nos. 333-111181 and 333-109564) of ArQule, Inc., of our report dated February 13, 2004 relating to the financial statements, which appears in this Form 10-K. /s/ PricewaterhouseCoopers LLP - --------------------------------- Boston, Massachusetts March 11, 2004