Flynn attended the College of the Holy Cross, where he played on the football team.

[1] In May 1921, the Loyola University New Orleans hired Flynn as its athletic director and football coach.

[2] He was tasked with starting up an athletics program at the school, and he coached the football team in its inaugural season in 1921.

[3] Although the Associated Press described the first season as "unsuccessful",[4] Flynn improved the team incrementally over his next two years.

[5] After three seasons at the helm, Flynn stepped down as coach and was replaced by Moon Ducote.