Mountcastle was elected to the National Academy of Sciences in 1966. In 1978, he was awarded the Louisa Gross Horwitz Prize from Columbia University together with David Hubel and Torsten Wiesel, both of whom received the Nobel Prize in Physiology or Medicine in 1981. In 1980, he was awarded the Ralph W. Gerard Prize in Neuroscience. In 1981, Mountcastle became a founding member of the World Cultural Council. In 1983, he was awarded the Albert Lasker Award for Basic Medical Research. In 1984, Mountcastle received the Golden Plate Award of the American Academy of Achievement. He also received the United States National Medal of Science in 1986. In 1998, Mountcastle was awarded the NAS Award in the Neurosciences from the National Academy of Sciences.