Columbia University’s provost, Alan Brinkley, is stepping down after five years on the job, leaving vacant a third major academic post for the university’s president, Lee Bollinger, to fill.

Mr. Bollinger already is searching for deans for both of Columbia’s undergraduate schools — Columbia College and the School of Engineering — and is forming a search committee to find a replacement for Mr. Brinkley. The next provost will oversee the university during its ambitious plan to expand into West Harlem.

In an e-mail message sent to students Wednesday night, Mr. Brinkley said that he has been honored to have played a part in an eventful period in Columbia’s life.

“But I feel that it is now time for me to return to research and teaching, and so I have informed the President that I will be leaving the provostship at the end of this academic year. I will of course continue to serve until a successor is named,” he wrote.

As the university’s chief academic officer, Mr. Brinkley was responsible for overseeing all of Columbia’s academic programs, faculty, and institutes. This included tenure decisions, which during Mr. Brinkley’s time have been the subject of much debate.

Last year, the provost was responsible for overseeing the tenure review of Barnard anthropology professor Nadia Abu El-Haj. The Palestinian-American professor, who was granted tenure last November, wrote a book that accused Israeli archaeologists of erroneous scholarship and defended the destruction of artifacts by Palestinians as “resistance.”

The same year, after a drawn-out public battle, it was reported that Middle East studies professor Joseph Massad was denied tenure. Mr. Massad has repeatedly argued that Zionism is “anti-Semitic” and that Israel is a “racist state that does not have a right to exist.”

Mr. Brinkley played a critical role in the decision to deny him tenure, overturning a narrow vote among a committee of five professors that supported Mr. Massad’s bid, according to the Chronicle of Higher Education. Mr. Brinkley’s refusal was met with an angry letter from several powerful faculty members, which moved Mr. Brinkley to reconsider, the Chronicle reported.

The office of the provost refuses to comment on the case, although a senior vice provost told the Columbia Spectator that it was “ongoing.”

Mr. Brinkley is an extremely popular professor and the subject of several adoring Facebook groups. His book about Father Coughlin, “Voices of Protest,” won a National Book Award in 1983.

Mr. Brinkley will remain provost until Mr. Bollinger finds his successor, and then will return to his position in the history department. Jonathan Cole, a sociology professor, previously held the position for 14 years.

The news of his departure caught students by surprise. A Columbia senior who is majoring in history, Eric Lukas, said he had waited three years to take a class with the popular professor. Yesterday, he sat through Mr. Brinkley’s lecture about 1920s America. “We didn’t know during class that this news was coming,” he said.