Thompson grew up in Rancho Santa Margarita, California, and was a standout defender at Trabuco Hills High School from 1995 to 1999, where he was a four-year Varsity starter, and earned all South Coast League 1st Team Honors for three years.
In Thompson's senior year the Mustangs earned a share of the South Coast League title and were knocked out of the quarter-finals of the CIF playoffs.
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.
When the Timbers were eliminated from the playoffs, Thompson returned to the Galaxy; however, he only made one appearance, playing a single minute.
History repeated itself in 2006: after an impressive performance in an exhibition match against English soccer team Coventry City, he was invited to a 10-day trial training session in August.