Thompson was selected in the 8th round of the 2003 Major League Baseball Draft by the Montreal Expos.

After the team Expos moved to Washington and became the Nationals in 2005, Thompson remained in Savannah for the year, pitching to a 3.35 ERA with 48 strikeouts in 53+2⁄3 innings of work.

[1] On July 13, 2006, the Reds traded Austin Kearns, Felipe López, and Ryan Wagner to the Washington Nationals for Thompson, Bill Bray, Royce Clayton, Brendan Harris, and Gary Majewski.

[2] After compiling a 2.22 ERA in the minors, Thompson was called up by the Reds on June 20, 2008, to replace the 0-3 Homer Bailey.

[5] On November 20, 2009, Thompson was outrighted to Louisville from the 40-man roster, and accepted his assignment with an invite to Spring Training.

[6] On May 26, 2011, Thompson was recalled to the majors when Matt Maloney was placed on the 15-day disabled list with a strained left oblique.

[11] After his release by the Twins, Thompson signed with the Southern Maryland Blue Crabs of the Atlantic League of Professional Baseball.

On August 20, 2013, Thompson signed a minor league contract with the New York Mets organization and was assigned to the Triple-A Las Vegas 51s.

[13] He recorded a 3.97 ERA in 9 appearances in Las Vegas and elected free agency on November 4.

Thompson returned to the Southern Maryland Blue Crabs after his stint with Oaxaca and turned in a 7–6 record and 4.76 ERA with 99 strikeouts in 22 appearances for the club.

[22] He started 27 games for Southern Maryland, logging a 15–4 record and 3.43 ERA with 119 strikeouts in 186+1⁄3 innings pitched.