Derksen was a highly rated prospect in his junior career. In spite of poor statistics with the Winkler Flyers, Derksen was twice named as the best goaltender in the MJHL. He was selected in the 3rd round of the NHL Draft and began attending the University of Wisconsin–Madison that fall. In his freshman season, Derksen served as a backup to future NHL All-Star Curtis Joseph, playing in only a quarter of Wisconsin's games. After Joseph turned pro after 1989, the team turned to Derksen as the starter and he came through in a big way. He improved his stats significantly and won a program record 31 games that season (still a Wisconsin record as of 2021). Derksen was instrumental in helping the Badgers finish first in the WCHA and was the top goaltender as Wisconsin won their conference tournament. Wisconsin received the second western seed and began the NCAA Tournament in the quarterfinals. Derksen was key in the Badgers winning two close games, particularly the national semifinal against Boston College, and made the championship game. Derksen wasn't as sharp in the final game but he didn't have to be. Wisconsin's offense overpowered the star-struck Colgate Raiders and the Badgers easily won the game 7–3.