In 1895, he took over as Nebraska's head football coach, posting a 6–3 record. In 1897, Thomas was the head football coach at Nebraska Wesleyan University. From 1901 to 1902, he served as the head football coach at Arkansas, where he compiled a 9–8 record.
Thomas took over as the top coach for Nebraska's football team in 1895, resulting in a 6-3 win-loss record. The following year, he led the Nebraska Wesleyan University team. From 1901 to 1902, Thomas managed the Arkansas football team, securing a 9-8 overall performance.