After one season as an assistant at
Notre Dame in 1946, Doherty became head coach at Arizona State, where he compiled a 25–17 record from 1947 to 1950. He left after ASU five days after defeating rival Arizona, 47–13, because he felt that he didn't have enough job security. In 1951, he coached at Rhode Island on a temporary basis after head coach
Hal Kopp was called to Army active duty. He compiled a 3–5 record in his only season as coach. From 1952 to 1954, Doherty coached high school football at
Punchard High School (1952) and
Lawrence High School in Massachusetts (1953–1954). He returned to college football in 1957 after one season as an assistant with the
Philadelphia Eagles. From 1957 to 1958, Doherty coached at Arizona, where he compiled a 4–15–1 record. Unlikely to be brought back for a third season, Doherty resigned and became head coach of
Xavier University. After two years out of the game, Doherty returned to coaching in 1964 as the head coach of
St. Augustine High School in
San Diego, California. From 1971 to 1975, he coached at Holy Cross, where he compiled a 20–31–2 record. After leaving Holy Cross, Doherty returned to Arizona, where he coached
Salpointe Catholic High School from 1978 to 1982 and was the school's athletic director until 1990. He coached the Lancers to the 1981 state championship game. ==Honors==