Flutie played football for Boston College, the only Division I-A school to recruit him, from 1981 to 1984, and won the Heisman Trophy, Maxwell Award, and the Davey O’Brien National Quarterback Award in his senior year (1984). Flutie became the first quarterback to win the Heisman since Pat Sullivan in 1971. Flutie left school as the NCAA’s all-time passing yardage leader with 10,579 yards and was a consensus All-American as a senior. He earned Player of the Year awards from UPI, Kodak, The Sporting News, and the Maxwell Football Club. The quarterback coach for Boston College from 1981 – 1983 was Tom Coughlin.

Flutie gained national attention in 1984 when he led the Eagles to victory in a high-scoring, back-and-forth game against the Miami Hurricanes (led by QB Bernie Kosar). The game was nationally televised on CBS the day after Thanksgiving and thus had a huge audience. Miami staged a dramatic drive to take the lead, 45–41, in the closing minute of the game. Boston College then took possession at its own 22-yard line with 28 seconds to go. After two passes moved the ball another 30 yards, only 6 seconds remained. On the last play of the game, Flutie scrambled away from the defense and threw a “Hail Mary pass” that was caught in the end zone by Gerard Phelan, giving BC a 47–45 win. Flutie won the Heisman trophy a week later, but the voting had finished before the game; Flutie said, however, that “without the Hail Mary pass I think I could have been very easily forgotten”.

The subsequent rise in applications for admission to Boston College after Flutie’s “Hail Mary” gave rise to the admissions phenomenon known as the “Flutie Effect”. This idea essentially states that a winning sports team can increase the recognition value of a school enough to make it more attractive to potential applicants.

In addition to his collegiate athletic achievement, Flutie maintained a distinguished academic record at Boston College. He was a candidate for a Rhodes Scholarship, for which he was named a finalist in 1984. Upon graduating, Flutie won a National Football Foundation post-graduate scholarship.

In November 2008, Flutie was honored by Boston College with a statue of him throwing his famous “Hail Mary” pass outside of Alumni Stadium. His number, 22, has been retired by the Boston College football program.