Flutie, who quarterbacked Boston College from 1981-84, holds nine school records, including most career passing yards with 10,579.
He is best remembered for his game-ending 48-yard touchdown pass to Gerard Phelan that beat Miami 47-45 as time expired in his final regular-season game.
Flutie played 13 seasons in the NFL and eight years in the Canadian Football League.
Others named to the Hall were Oklahoma center Tom Brahaney, Michigan defensive back Dave Brown, Clemson linebacker Jeff Davis, Texas defensive back Johnnie Johnson, Ohio State quarterback Rex Kern, Oregon running back/wide receiver Ahmad Rashad, Indiana running back Anthony Thompson, Houston defensive tackle Wilson Whitley, Dartmouth linebacker Reggie Williams.
They were joined by coaches Herb Deromedi and Joe Paterno, and will be inducted on Dec. 4 at South Bend, Ind.