In the autumn of 1986, Thomas accepted a scholarship to play football at Auburn University. His love of baseball drew him to the school's baseball team, where the coach immediately recognized his potential. "We loved him", Auburn baseball coach Hal Baird told "Sports Illustrated". "He was fun to be around—always smiling, always bright-eyed." He was also a deadly hitter, posting a .359 batting average and leading the Tigers in runs batted in as a freshman. During the summer of 1987 he played for the U.S. Pan American Team, earning a spot on the final roster that would compete in the Pan American Games. The Games coincided with the beginning of football practice back at Auburn, so he left the Pan Am team and returned to college—only to be injured twice in early season football games. In the summer of 1988, Thomas played for the Orleans Cardinals of the Cape Cod Baseball League. Highlights included a 3-homer game in Wareham, as well as a home run over the 434' sign in center field at Eldredge Park in Orleans. In 2000, Thomas was named a member of the inaugural class of the Cape Cod Baseball League Hall of Fame.