Eaton left Alma in 1956, and coached at Northern Michigan University for one year. From 1957 to 1961, Eaton served as defensive line coach at the University of Wyoming, and in 1962, he succeeded Bob Devaney as head coach there. In that role, he became one of the university's most successful coaches, compiling a record of 57–33–2. His greatest success came in the 1966, 1967, and 1968 seasons. In those three years, the team posted back-to-back 10–1 seasons, including a 14-game winning streak from November 5, 1966 to January 1, 1968, then followed this by going undefeated through the 1968 regular season. His teams won the 1966 Sun Bowl and played in the 1968 Sugar Bowl.