Following the close of his standout college career, Thompson chose to join the Bartlesville Phillips 66ers of the Amateur Athletic Union, though he was also drafted in the fifth round of the 1957 NBA Draft by the Minneapolis Lakers. Thompson had a successful career with the 66ers, earning AAU All-America honors three times and leading Phillips to an AAU title in 1962. He later coached the 66ers as well.
After his playing days were over, Thompson began the Gary Thompson Oil Company, a business venture made possible by his affiliation with the Phillips Petroleum Company. He also embarked on a 34-year television broadcasting career - serving as color commentator for college basketball games on NBC and CBS, primarily for Big Eight and later Big 12 games. He retired in 2006.