Michael Paul Thompson (born November 6, 1980) is a former Major League Baseball pitcher.
The 6'4 right-hander was selected by the San Diego Padres in the 5th round of the 1999 Major League Baseball Draft. In , Thompson showed his first signs of serious major league potential with the Double-A Mobile BayBears. That season, he went 10–2 with a 3.41 ERA.
Thompson started the season with the Triple-A Portland Beavers. He was called up to the Padres on May 17, , defeating the Arizona Diamondbacks in his major league debut. Thompson went on to start 15 more games for the big league club in 2006. In , he played in the Pittsburgh Pirates organization and became a free agent at the end of the season.