Prefontaine hoped to play quarterback in college football but could only obtain a scholarship as a punter at California State University, Fullerton. His punting average his first year led the state but the football program folded at the end of the season. Prefontaine received offers to play for multiple college football teams including Michigan, Michigan State, Georgia, LSU, and Texas but chose to go to Arizona State University because it was close to his family and friends. He was unhappy there, however, and left to go to San Diego State University. After a required redshirt year because of his transfer, he was named All-Conference as a punter in his junior year and first-team All-American as a punter in his senior year.