He served as head football coach at Stephen F. Austin State University (SFA) from 2007 to 2013, compiling a record of 37–45.
Harper was promoted to head coach of the Stephen F. Austin Lumberjacks from his position of defensive coordinator in December 2006.
It was the first time in ten years a Lumberjack squad had earned the SLC Championship trophy, and it was the program's first trip to the FCS playoffs since the 1995 season.
The 'Jacks recorded their second-straight top-10 national ranking, and advanced to the NCAA FCS playoffs for a second consecutive season where they hosted Villanova.
The Lumberjacks dominated the All-SLC teams, placing a league-best 21 players on the all-conference squad, including nine first-team selections.