Harper was the head college football coach for the AlmaScots located in Alma, Michigan. He held that position for the 1906 and 1907 seasons. His coaching record at Alma was 8 wins, 3 losses and 4 ties. As of the conclusion of the 2010 season, this ranks him #11 at Alma in total wins and #9 at the school in winning percentage (.667).
Harper was the 18th head college football coach for the Wabash College Little Giants located in Crawfordsville, Indiana, and he held that position for four seasons, from 1909 until 1912. His career coaching record at Wabash was 15 wins, 9 losses, and 2 ties. This ranks him tenth at Wabash in total wins and ninth at Wabash in winning percentage (.615). 
Harper is most known for his coaching at the University of Notre Dame. His 1913 football squad posted a 35–13 win over Army, one that is regarded by most football historians as the game that put Notre Dame on the football map.
Harper stepped down as head football coach after the 1917 season and returned to ranching in his home state of Kansas. His ranch was not far from where Knute Rockne was killed in a 1931 plane crash. Harper accompanied Rockne's body on the train from Kansas back to South Bend, Indiana, for the funeral and burial. The University of Notre Dame immediately hired Harper to fill Rockne's role as athletic director, a position in which remained until 1934, when Elmer Layden became head football coach and athletic director.
Harper was married and had two sons and one daughter.