Holton joined the Mountaineers in January of 1992 as the coach of the running backs from Northwestern where he was an assistant coach since 1989 working with the defensive backs, running backs, and receivers. He had also served as defensive coordinator for the Wildcats during the 1989 season.

Holton started his coaching career in 1971 as a graduate assistant at Iowa State, where he played collegiately. He also served as an assistant coach at Florida State in 1972 before joining Pitt's staff in 1973 as an assistant coach with linebackers and the defensive secondary. In 1979, Holton joined Jimmy Johnson's staff at Oklahoma State as secondary coach, a post he held until 1983, when he moved to Illinois where he served as an assistant coach for running backs, wide receivers and outside linebackers.