Shanafelt returned to Seattle to perform his residency in internal medicine at the University of Washington, where he received the Outstanding Resident Educator award. He later went on to a Hematology/Oncology Fellowship at Mayo Clinic, where he received both the Mayo Brothers Distinguished Fellow Award and the Summerskill award for outstanding scientific research. He spent the first 12 years of his career at the Mayo Clinic, where he served a three-year term as the president of the Mayo Clinic Voting Staff from 2013- 2016. In 2017, Shanafelt moved to Stanford, where he is a professor of medicine as well as the chief wellness officer of Stanford Medicine and associate dean at the Stanford School of Medicine.