Thompson made his final transfer to Fort Hays State University, where he was a two-time Academic All-American and a 1988 team captain.
[4] Thompson began his coaching career as a graduate assistant for the Mississippi State Bulldogs.
Thompson joined Steve Smith's staff as the hitting coach of the Baylor Bears in 1995, where he finally found a long-term home.
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.