Thompson was selected in the second round (16th overall) in the 2003 MLS SuperDraft by Los Angeles Galaxy. Unfortunately for Thompson, he tore his ACL in the preseason, and missed the entire 2003 season as a result. Returning healthy in 2004, Thompson was nevertheless unable to break into the Galaxy's starting lineup - he was loaned mid-season to the Portland Timbers of the A-League, where he excelled. Thompson started 13 games for the team, registering two assists, while helping lead the team to the A-League's best regular season record. When the Timbers were eliminated from the playoffs, Thompson returned to the Galaxy; however, he only made one appearance, playing a single minute.