Noonan attended Middlebury College, playing on the men's soccer team from 1979 to 1982.
In 2017, Noonan was inducted into the Middlebury College Athletics Hall of Fame for his playing time there.
[5] In 1989, Noonan was hired as head coach of the Wheaton College 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.