Bogged down for more than five months by a controversy surrounding a master’s degree improperly awarded to the governor’s daughter, the president of West Virginia University announced Friday that he would step down in September.

The decision follows an independent panel’s report in April that found that the university had shown “seriously flawed” judgment in awarding an M.B.A. to Heather Bresch, the daughter of Gov. Joe Manchin III, even though she did not have enough academic credits.

Ms. Bresch is a longtime friend and former business associate of the university president, Mike Garrison.

“During the last six weeks, we have found the university at the center of controversy and clamor,” Mr. Garrison said in a statement issued after a meeting of the university’s board of governors, which he attended, in Charleston. “I have made a decision to continue to serve as president of W.V.U. until September, because it is what a leader in this particular situation must do.”