In 2011 Allison won the Jacob Heskel Gabbay Award for Biotechnology and Medicine and was awarded the American Association of Immunologists Lifetime Achievement Award. In 2013 he shared the Novartis Prize for Clinical Immunology. In 2014 he shared the first Tang Prize in Biopharmaceutical Science with Tasuku Honjo, won the 9th Annual Szent-Györgyi Prize for Progress in Cancer Research of the National Foundation for Cancer Research, received the $3 million Breakthrough Prize in Life Sciences, the Canada Gairdner International Award, the Louisa Gross Horwitz Prize, and the Harvey Prize of the Technion Institute of Technology in Haifa. In 2015, he received the Lasker-DeBakey Clinical Medical Research Award. For 2017 he received the Wolf Prize in Medicine and the Balzan Prize for Immunological Approaches in Cancer Therapy (this prize jointly with Robert D. Schreiber). In 2018 he received the King Faisal International Prize in Medicine, the Jessie Stevenson Kovalenko Medal and the Albany Medical Center Prize in Medicine and Biomedical Research. He was awarded the Nobel Prize in Physiology or Medicine in 2018 jointly with Tasuku Honjo for their discovery of cancer therapy by inhibition of negative immune regulation.

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