Sheppard accepted an athletic scholarship to attend the University of Florida in Gainesville, Florida, where he played for coach Steve Spurrier's Florida Gators football team from 1999 to 2001. He was a first-team All-American as a sophomore in 2000, and a first-team All-Southeastern Conference (SEC) selection in 2000 and 2001. In his three-season college career, he started twenty-two games, recorded eight interceptions, had eighty-seven tackles, and returned twenty-seven kickoffs for 472 yards (an average of 22.5 yards per return). Sheppard declared himself eligible for the NFL Draft after his junior year.