In a letter to students, she called it the "right time for transition," according to the Harvard Crimson.
"It has been a privilege beyond words to work with all of you to lead Harvard, in the words of her alma mater, 'through change and through storm,'" she wrote, according to a university statement.
Faust, Harvard's 28th president, has held her role since 2007. Her appointment was groundbreaking - she was the first female president in the university's nearly 400-year history.
Faust assumed the presidency just as the world experienced a financial crisis, and it led it through the period to eventually set a college-fundraising record of more than $7 billion.
"Faust's intelligence, her depth, her warmth, her compassion, and her extraordinary ability to communicate - including her ability to listen to and understand what others are saying - are evidenced in all she does, and in how she leads," William F. Lee, senior fellow of the Harvard Corporation, wrote in a letter to the Harvard community, according to a statement from the school.
Harvard will begin a search committee the coming weeks to choose the next president, according to the Crimson. The process could take up to a year.