The college, which was founded in 1885 and has about 1,300 undergraduate students and 400 students in coed graduate programs, did not elaborate on the reasons for her departure.
In a letter to the Bryn Mawr community, McAuliffe wrote: "I have conferred with the board of trustees and will conclude my presidency at the end of this academic year."
"In the life of any institution, there are natural times for leadership change," she wrote.
There have been other high-profile administrative departures this academic year. Jenny Rickard, chief enrollment and communications officer, left in the fall. Elliott Shore, the chief information officer, also departed in the fall. And Donna Frithsen, who had been serving as a senior fund-raising adviser, left this winter to become associate vice president for advancement for Drexel's College of Medicine.
Janet Steinmayer, a member of the board of trustees' executive committee, said the other departures were unrelated to McAuliffe's.
In a statement, trustees credited McAuliffe with raising the college's profile nationally and internationally, adding interdisciplinary courses, improving the use of digital technology in the classroom, and other efforts.
"We've really been deliberating about the next steps and in consultation with Jane decided it was time to make a transition," Steinmayer said.
Asked for more specifics, Steinmayer said, "Being a college president is actually an intensive job. Getting the kind of success that we've had and will continue to have means it will continue to be an intensive job. We are going to continue to push forward and Jane has other things she'd like to do in her life."
The board plans to appoint an interim president for the 2013-14 academic year while the college conducts a national search.
McAuliffe said in her letter to the community that she planned to reflect, recharge, and finish a book.
Bryn Mawr becomes the second Philadelphia-area college to announce a presidential departure this month. Arcadia University last week announced it had terminated its president, Carl "Tobey" Oxholm III. Arcadia officials have not disclosed their reasons.
Contact Susan Snyder at 215-854-4693, at email@example.com, or on Twitter @ssnyderinq. Read her blog at http://www.philly.com/philly/blogs/campus_inq/.