Murphy was the 12th head coach at Northwestern University and he held that position for five seasons, from 1914 until 1918. His coaching record at Northwestern was 16–16–1. This ranks him 11th at Northwestern in total wins and tenth at Northwestern in winning percentage.
Murphy returned to coaching in the 1920 season to coach at the University of Denver, a coaching position he held for three seasons until 1922. At Denver, he compiled a record of 12–7–2. His best season at Denver was 1922, when the team's record was 6–1–1, second only to his 6–1 season at Northwestern in 1916.