Vančura was a member of the Communist Party of Czechoslovakia. As a response to the German occupation of Czechoslovakia, Vančura joined a secret communist resistance group in Autumn 1939. On May 12, 1942, at 5:00 a.m., the Gestapo assaulted his house in Zbraslav, arrested him and tortured him in the Prague Gestapo headquarters. On May 27, 1942, a commando of the Czechoslovak Foreign Army from Britain assassinated Reinhard Heydrich, Hitler's governor in Prague. As a result, there was a wave of reprisals: in the following weeks more than 2000 members of the Czech elite were executed. One of them was Vančura, executed by SS members in the military area Prague-Kobylisy on June 1, 1942 at 6:45 p.m. His body together with many others was disposed of secretly at Strašnice Crematorium.