Upon graduation, Noonan was selected in the first round of the 2003 MLS SuperDraft by New England Revolution. Although he started slowly, Noonan soon resumed his scoring ways, finishing his first season with the Revs with ten goals and seven assists, and runner-up to Damani Ralph for Rookie of the Year. Noonan did even better his sophomore year, scoring eleven goals and registering eight assists, tying with Amado Guevara for the MLS Scoring Champion Award. A late-season slump saw Noonan end 2005 with eight goals and seven assists. Noonan's 2006 campaign was marred by injury and he appeared in only 14 games, netting just one goal. He began 2007 injured once again and then became a substitute as he regained his fitness. However, he rounded into form and finished the season with 7 goals. 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.
On August 6, 2008 Noonan re-signed with MLS and was traded from New England, who still retained his rights, to Columbus Crew in exchange for the Crew's natural first-round selection in the 2009 MLS SuperDraft and allocation money. Additionally, the teams traded spots in the current 2008 allocation standings – with Columbus moving into the 10th spot and New England moving to third – and agreed to considerations regarding 2009 allocation rankings. For Columbus Crew, Noonan won the MLS Supporters' Shield, MLS Cup and Trillium Cup, all of them in 2008.
Noonan was traded to Colorado Rapids in June 2009. After making seventeen league appearances, Noonan was waived by Colorado on March 23, 2010.
Seattle Sounders
After a short trial with Seattle Sounders FC, Noonan signed with the club on March 30, 2010. He remained with Seattle through the 2011 season. At season's end, the club declined his 2012 contract option and he entered the 2011 MLS Re-Entry Draft.
LA Galaxy
Noonan was selected by Los Angeles Galaxy in stage two of the draft on December 12, 2011. Eleven days later he signed with Los Angeles. Noonan remained with Los Angeles through the 2012 season. 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. Noonan became a free agent after he went undrafted in both rounds of the draft. On January 11, 2013 LA announced that Noonan had retired as a player and had joined the club as an assistant coach.
International
Noonan earned his first cap for the United States national team on March 13, 2004 against Haiti. While he has accumulated 15 caps, injuries and inconsistency prevented him from claiming a major role with the national team. However, in early 2008 he started with the U.S. National Team against Sweden and registered an assist in a 2-0 victory. He has not played for the national team since 2008.
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.
Philadelphia Union
In January 2018, Noonan was hired as an assistant coach alongside Jim Curtin at the Philadelphia Union.
