"I have reluctantly concluded that the rifts between me and segments of the Arts and Sciences faculty make it infeasible for me to advance the agenda of renewal that I see as crucial to Harvard's future," Summers wrote in a letter posted on the school's Web site.
"This is a day of mixed emotions for me," he added in a conference call with reporters.
Effective at the end of the academic year, Summers' move brings to a close the briefest tenure of any Harvard president since 1862, when Cornelius Felton died after two years in office. Summers has led America's wealthiest university, with an endowment of more than $25 billion, since 2001.
He became embroiled in several controversies early in his tenure, among them the departure of prominent black studies professors such as Cornel West — who left after a falling out with the university president.
to an academic conference on women in science were a brief mention in a long speech, reports CBS News correspondent Sharyn Alfonsi but it made Crimson blood boil.
"It's a culture of political correctness, dominated by one point of view of the faculty," Professor of Government Harvey Mansfield told Alfonsi. "They don't like it when someone comes along and challenges them."
A broader debate emerged regarding Summers' management style, which some considered brusque and even bullying. He also was criticized by some for his handling of plans to expand Harvard's campus.
The discontent prompted a 218-185 no confidence vote from Harvard's Faculty of Arts and Sciences last March — the only known instance of such an action in the 370-year history of the university. Faculty votes are symbolic because the seven-member Harvard Corporation has sole authority to fire the university's president.
Another no confidence vote was scheduled for next Tuesday. It was called following the resignation of Faculty of Arts and Sciences Dean William Kirby: Some faculty believe he was pushed out by Summers, though Kirby has said the decision was mutual.
On Tuesday, Kirby issued a statement saying Summers had accomplished a great deal during his tenure, and "he has set in motion important initiatives for the university's future."