Noonan attended De Smet Jesuit High School, and played college soccer for the Indiana University Hoosiers from 1999 to 2002.

[3] He made his MLS debut in the 2003 season opener on April 13, coming on as a 92nd minute substitute for Daniel Hernandez in a 1-1 draw against the Chicago Fire.

[4] Although he started slowly, Noonan soon resumed his scoring ways, finishing his first season with the Revs with ten goals and seven assists in 28 appearances, and runner-up to Damani Ralph for Rookie of the Year.

Noonan also helped the Revolution win the 2007 U.S. Open Cup, the first piece of silverware in club history,[10] scoring a goal and providing two assists in the final.

[11] Noonan's option for the 2008 season was not picked up by New England and on January 23, 2008, he signed with Norwegian club Aalesunds FK.

After the conclusion of the 2012 season, LA declined the 2013 option on Noonan's contract and he entered the 2012 MLS Re-Entry Draft.

After Noonan's retirement as a player, he joined the Galaxy's technical staff as an assistant coach to Bruce Arena.

When Arena was announced as returning to be the head coach of the United States national team, he brought his supporting staff from the Galaxy, including Noonan, to work as assistants.

Noonan, along with new general manager Chris Albright, oversaw 24 player changes and the hiring of assistants Kenny Arena and Dominic Kinnear.

[citation needed] In the 2023 season, Noonan guided Cincinnati to their first trophy in MLS, finishing top of the league standings, clinching the Supporters' Shield and their second consecutive playoff berth.