In his freshman campaign at the University of Wisconsin–Madison for the Badgers men's ice hockey team, he made an immediate impact, leading all Badger freshmen in scoring with 12 goals and seven assists for 19 points. He also finished the season as the eighth-leading point-scorer for the team. Skille's goal 11:13 into the third overtime propelled the top-seeded Badgers past Cornell University 1–0 on March 26, 2006, in the NCAA Midwest Regional Final at the Resch Center, and into the team's first Frozen Four since 1992.