Joan de Beauvoir de Havilland was born on 22 October 1917, in Tokyo, Japan, to English parents. Her father, Walter de Havilland (1872–1968), was educated at the University of Cambridge and served as an English professor at the Imperial University in Tokyo before becoming a patent attorney. Her mother, Lilian Augusta Ruse de Havilland Fontaine (1886–1975), was educated at the Royal Academy of Dramatic Art in London, and became a stage actress who left her career after going to Tokyo with her husband. Her mother returned to work with the stage name "Lillian Fontaine" after her daughters achieved prominence in the 1940s. Joan's paternal cousin was Sir Geoffrey de Havilland (1882–1965), an aircraft designer known for the de Havilland Mosquito, and founder of the aircraft company which bore his name. Her paternal grandfather, the Reverend Charles Richard de Havilland, was from a family from Guernsey, in the Channel Islands.
De Havilland's parents married in 1914 and separated in 1919, when Lilian decided to end the marriage after discovering that her husband used the sexual services of geishas; the divorce was not finalized, however, until February 1925.
Taking a physician's advice, Lilian de Havilland moved Joan—reportedly a sickly child who had developed anaemia following a combined attack of the measles and a streptococcal infection—and her elder sister, Olivia de Havilland, to the United States. The family settled in Saratoga, California, and Fontaine's health improved dramatically.