Sullivan became UVa's first female president when she assumed that role two years ago.
In a statement, she cited "philosophical differences" with the board as a reason for her departure.
"It's been a great honor to serve as president of the University of Virginia," Sullivan said in the statement. "Although the board and I have a philosophical difference of opinion, I will always treasure having had the opportunity to work with so many gifted faculty and staff, talented students and loyal alumni. I am also grateful for the privilege to have worked with our extraordinary vice presidents and deans."
In the same statement, the university's Board of Visitors said it expected to quickly name an interim president and begin a search for a new leader.
Newplex.com reported the board planned to hold an emergency closed door meeting at 2:00 p.m Sunday.