She played college basketball for the Michigan Wolverines, where she is Michigan's all-time leading scorer in points, man or woman, with 2,776 career points, field goals made, three-point field goals made, double-figure scoring games and 30-point games.

[6] For her senior year she then transferred to Metuchen High School where her father and uncle played.

[7] She suffered a Lisfranc injury early in the season, that prematurely ended her high school playing career.

On January 7, 2017, she scored a career-high 38 points and set a then program-record with eight three-pointers in a game against Ohio State.

[11] Following the season she was named a unanimous All-Big Ten first team selection by both the coaches and the media for the second consecutive year.

She helped Michigan advance to the NCAA Division I women's basketball tournament for the first time since 2013.

Following an outstanding season, she was named a finalist for the Nancy Lieberman Award and University of Michigan Female Athlete of the Year.

[25] Flaherty finished her career at Michigan as the all-time leading point-scorer in Michigan basketball history, man or woman, with 2,776 career-points, field goals made (984), three-point field goals made (410), double-figure scoring games (127) and 30-point games (13).