WASHINGTON — The World Bank president, Paul Wolfowitz, will resign at the end of June, he and the bank said late yesterday, ending his long fight to survive pressure for his ouster over the generous compensation he arranged for his girlfriend.

His departure ends a two-year run at the development bank that was marked by controversy from the start, given his previous role as a major architect of the Iraq war when he served as the no. 2 official at the Pentagon.

“He assured us that he acted ethically and in good faith in what he believed were the best interests of the institution and we accept that,” the board said in its announcement of Mr. Wolfowitz’s resignation.

Mr. Wolfowitz was all but forced out, however, by the finding of a special bank panel that he violated conflict-of-interest rules in his handling of the 2005 pay package of bank employee Shaha Riza.

The controversy, which gripped the bank for a month, was seen as a growing liability that threatened to tarnish the institution’s reputation and hobble its ability to persuade countries around the world to contribute billions of dollars to provide financial assistance to poor nations.

By tradition, the World Bank has been run by an American. The Bush administration keenly wanted to keep that decades-old practice firmly intact as the board dealt with Mr. Wolfowitz’s fate. America is the bank’s largest shareholder and its biggest financial contributor.

The White House said it would have a new candidate to announce soon, allowing for an orderly transition.

Earlier yesterday, President Bush had seemed resigned to the likelihood that Mr. Wolfowitz would lose his job over the conflict-of-interest charges. “I regret that it’s come to this,” Mr. Bush said.

In its statement, the bank’s board said it was clear that a number of people had erred in reviewing Ms. Riza’s pay package.