Thompson was drafted out of high school in the first round of the 1991 MLB draft and started his career in Detroit Tigers minor league system. Thompson started his pro career with the rookie class Bristol Tigers of the Appalachian League in 1991. Thompson moved up to class "A" the next year joining the South Atlantic League's Fayetteville Generals in 1992. In 1993 Thompson split time in A and AA, playing with the Lakeland Tigers of the Florida State League and the Eastern League's London Tigers. He made his Major League debut in 1996. He was selected to the American LeagueAll-Star team in 1997, at the age of 24, during a 15 win, 11 loss season, in which he also finished fifth in the league with a 3.02 ERA. Injury problems, however, sent him to the minor leagues soon after his start.
Thompson was traded by the Tigers to the Rangers in an eight player trade after the 1999 season which involved Juan González being sent to Detroit. He spent six seasons in the Minors with the Rangers organization, including a missed 2001 season due to a torn rotator cuff suffered in 2000, before playing in the Majors again for two games in 2005. Thompson elected free agency after the 2005 season and subsequently signed a minor league contract with the Milwaukee Brewers in December 2005. In May 2006, he retired after playing eight games for the Brewers's Triple-A affiliate, the Nashville Sounds.