Johnson began his coaching career as an assistant at Sylvan Hills and Arkansas Baptist High School before landing the head coaching job and winning a state championship at Abundant Life School in Sherwood.[4] He has served as a pitching coach for the Central Arkansas Bears and Dallas Baptist Patriots, before joining the Mississippi State Bulldogs in 2016. He spent one season with Mississippi State before he was hired to coach the Arkansas Razorbacks pitchers.[5] After the 2018 season, the Minnesota Twins of Major League Baseball hired him as their pitching coach.[3][6]
On June 26, 2022, Johnson was announced as the new pitching coach of the LSU Tigers. Leaving his pitching coach role with the first-place Twins for the same position at the NCAA level was reported as a rare move by many in the media, including Jeff Passan.[7]
On June 5, 2023, Johnson was hired as the Georgia Bulldogs head baseball coach.[8]
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