He reached the height of his success in 1940, in his first season at Stanford, where he led the Indians to an undefeated season that culminated with a Rose Bowl victory. That year, he also helped prepare the Chicago Bears for the 1940 NFL Championship Game, in which they routed Washington, 73–0. Shaughnessy's successes showcased the effectiveness of the T formation and encouraged its widespread adoption. He was inducted into the College Football Hall of Fame in 1968. Shaughnessy also coached college basketball at Tulane University. He played college football at the University of Minnesota.