From 1923 to 1929, Wray served as an assistant football coach at Penn. In 1930 he succeeded Lou Young as head coach. He was fired on December 12, 1930, due to friction with players, alumni, and the public.
In 1932, Wray was named head coach of the Boston Braves, a National Football League expansion team. The Braves went 4–4–2 in their inaugural season. He left the team after one season and was replaced by Lone Star Dietz.
In 1933, Wray's former teammate and fellow assistant at Penn, Bert Bell convinced him to become coach of the expansion Philadelphia Eagles. By 1936, the club was suffering significant financial losses and was offered for sale at a public auction. Bell was the only bidder and became the team's sole owner. On April 28, Wray refused a 66% reduction in salary and left the team.
In 1938, Wray became an assistant at Manhattan College. He remained with the school until his resignation in November 1940. In 1941, Wray served as an assistant to Anthony H. Scanlan at Saint Joseph's University. When Scanlan became head coach at Holy Cross, Wray followed him. In 1943, Scanlan's war commitments limited him to only being able to coach on game day and Wray led the team the rest of the week. Wray and Scanlan had a falling out and Wray was replaced by Ox DaGrosa for 1944.