A line drive hitter and versatile defensive player, Wilkerson attended the University of Florida and was selected by the Montreal Expos in the first round (33rd pick) of the 1998 Major League Baseball Draft. The Gators made a return trip to the CWS two years later in Wilkerson's junior year. As a junior, he became the first player in college history to hit 20 home runs, steal 20 bases, and win 10 games as a pitcher in the same year. He was named the College Player of the Year by Rotary Smith.