Flynn was married three times: first to actress Lili Damita from 1935 until 1942 (one son, Sean Flynn, 1941–70?); to Nora Eddington from 1943 until 1949 (two daughters, Deirdre born 1945 and Rory born 1947); and to actress Patrice Wymore from 1950 until his death (one daughter, Arnella Roma, 1953–1998).