Cowan, who also became a director at the Chantilly, Va., banking technology vendor, was most recently the CEO at Interwoven Inc., a content-management software company that was purchased by Autonomy Corp PLC last year.
He has also been the CEO at Manugistics Group and EXE Technologies.
"Joe has a history of guiding companies through challenging situations by implementing successful business strategies," John Dorman, Online Resources' chairman, said in a press release last week.
Cowan was hired June 15. He succeeds Dorman, who has been the interim CEO since April.
Online Resources has been searching for a permanent CEO since its founder, Matthew P. Lawlor, left in December.
Online Resources initially assigned Raymond T. Crossier, its president and chief operating officer, as the interim CEO; Crosier left Online Resources in April.
It still does not have a COO.
Lawlor's departure was described as a retirement, but observers suspected his leaving was related to the company's performance.
Lawlor also lost a proxy battle last year with the hedge fund Tennenbaum Capital Partners LLC, which elected three directors, including Dorman, to Online Resources' board.
