Thompson was the Bulldogs' offensive coordinator and quarterbacks/B-backs coach for the last two seasons. The Citadel produced 27 individual 100-yard rushing games in that time - the most in any two-year stretch in school history - including a program-record 14 in 2015.
"This is a fantastic day for me and my family," Thompson said. "I'm honored to be the new head coach at The Citadel. ... I'm looking forward to continuing the success we have begun to establish within the program, and it is important to me that we maintain continuity to give our cadet-athletes the best chance to succeed on the field and in life. We will build on the achievements from the last two seasons and represent The Citadel the proper way."
Houston went 14-11 in two years, including 9-4 this past season when he led the Bulldogs to a share of the Southern Conference title and their first FCS playoff appearance since 1992.