Jeptoo finished Monday's race in a course-record 2 hours, 18 minutes, 57 seconds. She becomes the seventh three-time Boston Marathon champion.
Jeptoo broke away from a group of five runners at the 23-mile mark. Buzunesh Deba finished second with an unofficial time of 2:19:59.
American Shalane Flanagan finished fifth after leading for more than half the race.
Lanni Marchant of London, Ont., was the top Canadian in 14th.