His work has been recognized by many awards including the Burroughs Wellcome Fund Career Award for Medical Sciences, the AACR Gertrude B. Elion Award, the HHMI Faculty Scholar Award, and an NCI Outstanding Investigator Award. Vander Heiden serves on the scientific advisory board of Yale Cancer Center, the Ellen and Ronald Caplan Cancer Center at the Wistar Institute, and Salk's Cancer Center, as well as Agios Pharmaceuticals, Auron Therapeutics (of which he is also an academic founder), iTeos Therapeutics, Sage Therapeutics, Lime Therapeutics, and Pretzel Therapeutics. He is part of the investment advisory board for DROIA Venture Fund.