Following his graduation from Texas Tech in 1966, Wilson became an assistant coach at Texas Tech under King and Jim Carlen, before heading to Texas A&M to join the coaching staff of Emory Bellard. After Bellard resigned in the midst of the 1978 season, Wilson was appointed head coach of the Aggies on October 24, 1978. He led the Aggies to a win in the 1981 Independence Bowl. He amassed a record of 21–19 during his three and a half seasons, before being replaced by Jackie Sherrill in 1982.
In 1984 Wilson returned to his alma mater as offensive coordinator under Jerry Moore. Moore had coached Wilson at Corsicana as an assistant under Acree. In 1986, Wilson left the collegiate ranks, coaching at Palestine High School. Finally, in 1993, he took over head coaching duties at his alma mater Corsicana, coaching the Tigers until his retirement in 1999. As a proponent of the running game, Wilson permitted Ketric Sanford to carry the ball 1,058 times during his career at Corsicana (1993–1995), which is third all-time in Texas behind Robert Strait and Billy Sims. Wilson guided Corsicana to the 1997 4A Division I state championship game versus Texas City, but lost 34–37.