Thompson was born in Saint Paul, Minnesota, spent early years on his family's farm, and received his early education at St. Paul Academy and Avon Old Farms School, a progressive school founded by architect Theodate Pope Riddle in Avon CT.
Near the end of the war, Thompson's ship docked in Boston and he was introduced to Walter Gropius, founder of the Bauhaus School and then head of the Harvard Graduate School of Design.