In 1989, he was hired as head coach of the Wheaton College men's soccer team. The team had a 4-11-0 record his first season, but he took them to a 12-5-1 record his second season. This led to a move to the University of New Hampshire where he coached from 1991 to 1994. In 1995, he became head coach of the Brown University's men's soccer team. Noonan compiled a 160-77-31 record with ten NCAA post-season tournament appearances in fifteen seasons with the Bears. On January 5, 2010, Clemson University announced they had hired Noonan as head coach of the men's soccer team.