Freuchen was born in Nykøbing Falster, Denmark. His father was Lorentz Benzon Freuchen (1859 - 1927), a Danish Jew, and his mother was Anne Petrine Frederikke Rasmussen (1862 - 1945).
Freuchen married three times. First, in 1911, to Navarana Mequpaluk (d. 1921), an Inuit 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, in 1924, to Magdalene Vang Lauridsen (1881-1960) was dissolved in 1944. Lastly, in 1945, he married Dagmar Cohn (b. 1907).
Freuchen's Danish island estate was named Enehoje.
He spent many years in Thule, Greenland, living with the Polar Inuit. He worked with Knud Rasmussen, crossing the Greenland icecap with him. In 1935, Freuchen visited South Africa, and by the end of the decade, he had travelled to Siberia.
In 1938 he founded The Adventurer's Club (Eventyrernes Klub in Danish), which still exists. They later honoured his memory by planting an oak tree and creating an Eskimo cairn near the place, where he left Denmark for Greenland back in 1906. (It is situated East of Langeliniebroen in Central Copenhagen and not far from the statue of The Little Mermaid).
He was also employed by the movie industry as a consultant and scriptwriter, specializing in Arctic-related scripts. Most notably MGM's Oscar winning Eskimo/Mala The Magnificent starring Ray Mala. In 1956, he won $64,000 on The $64,000 Question, an American TV quiz-show on the subject "The Seven Seas".
During World War II, Freuchen was actively involved with the Danish resistance movement against the Germans, despite having lost a leg to frost bite in 1926. He was imprisoned for a time by the Germans.
Freuchen and his wife Dagmar, a fashion illustrator, lived in New York City, and maintained a second home in Noank, Connecticut.
The preface of his last work, Book of the Seven Seas, is dated August 30, 1957, in Noank. He died of a heart attack three days later in Elmendorf, Alaska. After his death, his ashes were scattered on the famous table-shaped Thule Mountain near the USAF base.