Temple University President Neil Theobald resigned Thursday, hours before the Board of Trustees was expected to dismiss him.
Richard Englert is now interim president.
Trustees last week took a vote of no confident in Theobald and announced their intention to let him go.
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The vote was unanimous among the 34 of 36 trustees present, board spokesman Kevin Feeley said.
The action comes less than a month after the removal of provost Hai-Lung Dai amid a $22 million financial aid shortfall, and Feeley said the decision was largely based on Theobald's handling of Dai's removal and the deficit.
Feeley told The Philadelphia Inquirer that the financial problem was known a year ago when the deficit was $9 million, but Theobald allowed it to grow rather than correct it.
Trustees were set to vote on dismissing Theobald, who has led the university for 3½ years, and planned to appoint as acting president chancellor Richard Englert, a former provost who has served as acting president before.
Temple law school dean JoAnne Epps was named provost last week.