He left the Quakes before the 2005 season, traded to Dallas in a large deal that included Arturo Alvarez and Brad Davis.

On March 20, 2007, Mulrooney was traded to expansion MLS club Toronto FC, in exchange for a partial allocation and a 2008 SuperDraft first-round pick.

Mulrooney played every game the remainder of the season for the Dynamo and tied for the team lead with five assists.

Despite his success in MLS, Mulrooney has struggled to earn time for the US national team, as Claudio Reyna, John O'Brien, Pablo Mastroeni and Chris Armas play his position.

In a friendly match versus Ireland in Dublin during the lead-up to the tournament there was a torrential downpour which severely hampered play.