Bardeen was awarded the 1996 J.J. Sakurai Prize of the American Physical Society for his work on anomalies and perturbative quantum chromodynamics. In 1985, he was awarded a John S. Guggenheim Memorial Foundation Fellowship for research on the application of quantum field theory to elementary particle physics. Previously, he had received the Senior Scientist Award of the Alexander von Humboldt Foundation and an Alfred P. Sloan Foundation Fellowship for research in theoretical physics.