Freeney received an athletic scholarship to attend Syracuse University, where he played for the Syracuse Orange football team from 1998 to 2001. A two-year starter for the Orangemen, he set a school record with 17.5 sacks in his senior season and his 34 career sacks rank second in school history to Tim Green (45.5). Freeney was the school's premier pass rusher, and once had a string of 17 consecutive games with at least one sack. Against Virginia Tech, Freeney sacked elusive Hokies quarterback Michael Vick 4.5 times in one game.