Warren was the first dean of Harvard Medical School (1816–1819) and promoted its move from Cambridge to Boston. Harvard presented him with an honorary medical degree in 1819. He was a founding member of Massachusetts General Hospital and served as the facility's first surgeon. He held an appointment on the hospital staff until 1853 and was then on its Board of Consultation until his death. Over the course of his long career, Warren assembled an extraordinary teaching collection of anatomical and pathological specimens, which he presented to Harvard in 1847 along with $5000. This was the beginning of the Warren Anatomical Museum.