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 class "A" and class "double A" playing with the Lakeland Tigers of the Florida State League and the Eastern League's London Tigers. He was selected to the American League All-Star team in at the age of 24 during a 15 win, 12 losses season in which he also finished fifth in the league with a 3.02 ERA.
Injury problems, however, plagued him and sent him to the minor leagues soon after his bright 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 , 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 2006, he was on the roster of the Brewers Class AAA affiliate, the Nashville Sounds, however, he retired from baseball in May 2006.