Thompson began his coaching career as a graduate assistant for the Mississippi State Bulldogs. He moved to Virginia in 1991, working as a paid assistant for the Radford Highlanders. He returned to Mississippi State for the 1992 and 1993 seasons.[5] He would also join the Auburn Tigers for a season in 1994.
Thompson joined Steve Smith's staff as the hitting coach of the Baylor Bears in 1995, where he finally found a long-term home.[6] After 15 years on Smith's staff, he was promoted to Assistant head coach. Following the 2013 season, he accepted the head coaching position at McLennan Community College.
On June 15, 2022, Thompson was named the head coach of the Baylor Bears.[7]
National champion
Postseason invitational champion
Conference regular season champion
Conference regular season and conference tournament champion
Division regular season champion
Division regular season and conference tournament champion
Conference tournament champion