Freuchen was married three times. He was first married in 1911 to Navarana Mequpaluk (d. 1921), an Inuk woman who died in the Spanish Flu epidemic after bearing two children (a boy named Mequsaq Avataq Igimaqssusuktoranguapaluk (1916 - c. 1962) and a girl named Pipaluk Jette Tukuminguaq Kasaluk Palika Hager (1918–1999)). His second marriage was to Magdalene Vang Lauridsen (1881–1960), daughter of Johannes Peter Lauridsen (1847-1920), Danish businessman and director of Danmarks Nationalbank. The marriage started in 1924 and was dissolved in 1944. In 1945, he married Danish fashion illustrator, Dagmar Cohn (1907–1991).