McDonald and Yoji Totsuka were awarded the 2007 Benjamin Franklin Medal in Physics "for discovering that the three known types of elementary particles called neutrinos change into one another when traveling over sufficiently long distances, and that neutrinos have mass".
He later became the Director of the Kamioka Observatory, part of the Institute for Cosmic Ray Research (ICRR) at the University of Tokyo in 1995 and then Director of the Institute for Cosmic Ray Research in 1997.