Born in Žamberk in northeastern Bohemia, Eben spent most of his childhood and early adolescence in Český Krumlov in southern Bohemia. There he studied piano, and later cello and organ. The years of World War II were especially difficult for the young man. Although Eben was raised as a Catholic, his father was a Jew and thus fell foul of the National Socialist occupiers of his homeland. In 1943, aged 14, Eben was captured and imprisoned by the Nazis in Buchenwald, remaining there for the duration of the war.