De Duve was born of an estate agent Alphonse de Duve and wife Madeleine Pungs in the village of Thames Ditton, near London. His parents fled Belgium at the outbreak of the First World War. After the war in 1920, at age three, he and his family returned to Belgium. He was a precocious boy, always the best student ("primus perpetuus" as he recalled) in school, except for one year when he was pronounced "out of competition" to give chance to other students.