Jean Charlot was born in Paris, France on October 29, 1868. He studied at the École des Beaux Arts in Paris before serving in the French Army during World War I. His maternal grandfather was a French-Indian mestizo and his mother, Anna, was an artist. After Charlot's father died in 1921, he and his mother moved to Mexico City and he became fascinated with Mexican art and manuscripts and studied the Aztec language. Charlot sketched for archeologists excavating Mayan ruins and he assisted Diego Rivera and other members of the Syndicate of Painters and Sculptors on a series of mural paintings in Mexico City.

Charlot and his mother moved to the United States in 1928. After working in 1929 with lithography printer George Miller in New York, Charlot began a lifetime collaboration in 1933 with Lynton R. Kistler, master lithography printer in Los Angeles, reputedly making the first stone-drawn color lithographs in the United States. Between 1934 and 1935, Charlot worked for the WPA Federal Arts Project and painted murals for the Straubenmuller Textile High School in Manhattan. In 1944, Josef Albers invited Charlot to teach at the Summer Institute of Black Mountain College and, in 1947, he headed the art school at the Colorado Springs Fine Arts Center, and worked with Lawrence Barrett printing lithographs. In 1949, he moved to Hawaii where he taught at the University of Hawaii at Manoa. Charlot died in Honolulu, Hawaii on March 20, 1979.