Thomas began his coaching career at his alma mater Texas Tech as a student assistant from 1998 to 2001, before becoming a graduate assistant at Midwestern State. He worked with the wide receivers during his time as the team's graduate assistant. He served one season as the passing game coordinator and quarterbacks coach for the Mustangs before being promoted to offensive coordinator in 2005.[2]
Thomas left the Mustangs to join the Atlanta Falcons on newly hired head coach Mike Smith's coaching staff. He spent 4 seasons as an offensive assistant before being promoted to the team's quarterbacks coach in 2012.
After Falcons head coach Mike Smith was fired, Thomas was not retained by Dan Quinn. Thomas was then hired by Matt Rhule to coach quarterbacks for Temple. Marcus Satterfield, Temple's offensive coordinator shifted from coaching quarterbacks to running backs after the hire of Thomas.[3] After Satterfield was hired to be the next head coach at Tennessee Tech, Thomas was promoted to offensive coordinator.[4]
After Rhule was hired to be the next head coach at Baylor in 2017, Thomas joined him as the Bears' co-offensive coordinator and quarterbacks coach, sharing coordinator duties with Jeff Nixon. After Rhule left Baylor to be the head coach of the Carolina Panthers in 2020, Thomas was hired by newly hired Memphis head coach Ryan Silverfield to be a senior offensive analyst, a role he held for two months.[5][6]
When UNLV's passing game coordinator and quarterbacks coach Danny Langsdorf left to accept an assistant coaching position at Colorado, Thomas was hired as the team's offensive coordinator and quarterbacks coach on April 23, 2020.[7][8]
After Zak Hill resigned from Arizona State following several allegations of recruiting violations, Thomas was announced as offensive coordinator and quarterbacks coach on January 31, 2021.[9]
On April 5, 2023, Thomas was announced as being hired as an offensive assistant for the Pittsburgh Steelers
On January 16, 2024, Thomas was announced as being hired as the co-offensive coordinator and quarterbacks coach for the Nebraska Cornhuskers