After his two years work for the navy, Folkman completed his residency at Massachusetts General Hospital. He worked as an assistant surgeon at Boston City Hospital, then trained further in pediatric surgery at Children's Hospital of Philadelphia under C. Everett Koop. In 1967 he was appointed surgeon-in-chief of Children's Hospital Boston at the age of 34. Folkman was appointed the Julia Dyckman Andrus Professor of Pediatric Surgery at Harvard Medical School in 1968, where he was also Professor of Cell Biology. He was the youngest full Professor at Harvard Medical School in history. In addition to directing the Children's Hospital Boston Surgical Research Laboratories, which grew to become the Vascular Biology Program, for nearly four decades, he was the Scientific Director of the hospital's Vascular Anomalies Center.