Thompson was the seventh head football coach for the Lehigh Mountain Hawks in Bethlehem, Pennsylvania and he held that position for two seasons, from 1898 until 1899. His overall coaching record at Lehigh was 5 wins, 15 losses, and 1 tie. As of completion of the 2007 season, this ranks him 17th at Lehigh in terms of total wins and 25th at Lehigh in terms of winning percentage. Highlights of his two seasons included back-to-back victories over rival Rutgers.