Magoun was born to a prosperous family in New York City. His parents were Francis Peabody Magoun (1865–1928) and Jeanne C. Bartholow (1870–1957). He received his primary education at the St. Andrew's School in Concord, Massachusetts, and at the Noble and Greenough School in Boston. He took his bachelors degree at Harvard in (1916), and in February of that year signed on with the American Field Service. From 3 March – August 3 he was a volunteer ambulance driver.