After graduating with his masters, he spent one year as an assistant at the University of New Hampshire under coach Bob Kullen, but Kullen fell ill and that left his job in jeopardy. Seeking stability, he accepted a position as an assistant coach at his alma mater in 1988, a position he held through the 1998–99 school year. During that time, the Falcons made three NCAA tournament appearances. Several players went on to successful careers in the National Hockey League.
In 1999, after five years of seeking a head-coaching position, he was hired to be head coach at Division III Rochester Institute of Technology. He led the RIT Tigers to a nearly-undefeated season in 2000–01; their only loss was on home ice in the 2001 national championship game. That year, he won the Edward Jeremiah Award for the top coach in Division III men's hockey. In his first six years at RIT, he compiled a 116–31–12 record, with four ECAC West regular-season championships, three ECAC West tournament titles, and three NCAA tournament appearances. However, those all came in his first years at RIT; in 2003, the Tigers missed the D-III national tournamentfor the first time since 1995, and they would never return. In late 2004, despite a couple of "down" years for the program, RIT President Albert J. Simone announced that RIT would move their hockey program up to the Division I level, retaining Wilson as head coach. RIT would join Atlantic Hockey starting in the 2006–07 season. The rest of the 2004–05 campaign was rough, and the Tigers finished with their worst record of Wilson's tenure to date, including a painful loss to arch-rival Elmira College in which the Tigers squandered a late two-goal lead by allowing a pair of short-handed goals in the last three minutes of regulation. They would eventually lose in overtime 7–6. The Tigers' first season as a Division I program, in which they played as an independent was even harder, although the highlight was a home win over the St. Lawrence Saints thanks to a 66 save performance by goaltender Jocelyn Guimond. The Tigers won only nine games that season, mostly against future Atlantic Hockey conference opponents. Since joining Atlantic Hockey in 2006, though, success has been the Tigers' hallmark. They won three regular-season conference championships in four years, and in 2010 they won their first conference tournament. That granted them the conference's autobid into the national tournament, where they stunned Denver and New Hampshire to win the East Regional and advance to the Frozen Four. In 2010, in recognition of reaching the Frozen Four, Wilson won the Spencer Penrose Award, for the top coach in Division I men's ice hockey. He became the first coach to win both the Spencer Penrose Award and the Edward Jeremiah Award. He also signed a five-year contract that year, keeping him at RIT until at least the 2014–15 season. During the 2014–15 season, Wilson led the Tigers to their second NCAA tournament appearance at the Division I level, where they knocked off the #1 overall seed Minnesota State Mavericks in the first round. Following the end of the 2014–15 season, Wilson signed a seven-year contract extension with RIT, through the 2022 season. During the 2015–16 season, Wilson led the Tigers to a third NCAA tournament appearance at the Division I level where they faced the #1 overall seed Quinnipiac Bobcats. Unlike the previous season, there would be no upset as the Tigers were shutout 4–0. In ten seasons of Division I play, Wilson has led the Tigers to several victories over nationally ranked teams. Under Wilson's tutelage, the Tigers have defeated at least one nationally-ranked team in nine out of ten Division I seasons. As Head Coach, 35 players went on to sign professional contracts. Notables include Steve Pinizzotto in 2007 who became the first RIT Tiger to sign an NHL contract at the Division 1 level. Chris Tanev signed with the Vancouver Canucks in June 2010 and became the first RIT alumnus to play in the NHL making his debut on January 18, 2011. He has also made his playoff debut in the 2011 Stanley Cup Finals suiting up in the Conference Finals for games 3, 4 and 5, and in the Stanley Cup Finals for games 5, 6 and 7. Tyler Brenner signed with the Toronto Maple Leafs in March 2011 on a two year entry level contract.
