During his college years Thompson also played with Carolina Dynamo in the USL Premier Development League.

[5] In his rookie campaign, Thompson made 27 regular season appearances, and started all four of the Revolution's playoff matches, providing a game-winning assist in the 2007 Eastern Conference final, setting up Taylor Twellman's famous bicycle kick.

[12] On January 22, 2010, the Revolution traded Thompson to the Colorado Rapids along with Jeff Larentowicz in exchange for a third-round pick in the 2011 MLS SuperDraft, Preston Burpo and Cory Gibbs.

[3] On April 14, 2010, Thompson scored his first two goals for Colorado in a 2–1 victory over Kansas City Wizards in a 2010 Lamar Hunt U.S. Open Cup qualification match.

[16][17] Thompson was named the Rapids' 2011 Humanitarian of the Year, and was one of only two players to appear in all six of the club's 2011 CONCACAF Champions League matches.

[24] After Charlotte Eagle's move down to the USL PDL, Thompson signed with Carolina RailHawks on February 3, 2015.