Charlot was born in Paris. His father, Henri, owned an import-export business and was a Russian-born émigré, albeit one who supported the Bolshevik cause. His mother Anna was herself an artist. His mother's family originated from Mexico City, his grandfather a French-Indian mestizo.
Charlot spent an extensive period of his life living and working in Mexico. In 1921, he and his mother left Europe to settle in Mexico City. He met Fernando Leal (1896–1964) and shared his studio with him. He also started avant-garde woodcuts and, after Leal's invitation, participated in the founding of Mexican muralism with his fresco "The Massacre of the Templo Mayor" (1921–1922), in front of Fernando Leal's "The Dancers of Chalma" (1921–23). In his fresco Charlot portrayed himself, Leal and Rivera. He also worked as an illustrator during the excavations at Chichen Itza under Sylvanus Morley.
In 1940, Charlot applied for and was accorded American citizenship. A dual citizen of the United States and France, he retained passports from both countries.
He spent some time working for the Work Projects Administration's Federal Arts Project, including creation of murals for Straubenmuller Textile High School in Manhattan during 1934-1935. In 1942 he painted an oil on canvas mural for the post office in McDonough, Georgia: "Cotton Gin", 4.5 ft × 11 ft (1.4 m × 3.4 m). In 1949, Charlot relocated to Hawaii to become a professor of art at the University of Hawaii at Manoa. He continued to live and work there until his death in 1979. Abstract Expressionist Kenneth O. Goehring and Jean's son Martin Charlot were among his students.
Charlot came to Colorado Springs, Colorado in 1947 to take the job as Head of the Art School of the Colorado Springs Fine Arts Center. He taught fresco painting and worked with Lawrence Barrett on several editions of lithographs. While there he also taught art at The Fountain Valley School, an independent school for boys (at that time), founded in 1930. Charlot left the Fine Arts Center in 1949 under a cloud of misunderstandings between himself and the Arts Center's Board or Trustees and the Art Center's director, Mitch Wilder. Charlot then went to teach at the University of Hawaii where he stayed for over 30 years, teaching art. During the summer of 1969, Charlot worked with Tony Smith at UH and Smith thanked him by creating a piece in the For... series for Charlot; For J.C.
The Fine Arts Museums of San Francisco, the Cleveland Museum of Art, the Hawaii State Art Museum, the Honolulu Museum of Art, the Isaacs Art Center (Waimea, Hawaii), and the University of Hawaii at Manoa library are among the public collections having works by Jean Charlot.
In 1926 Charlot published "An Artist on Art: Collected Essays of Jean Charlot", which discussed Mexican art history 
In 1940 he illustrated the book Tito's Hats (Garden City Publishing), which was written by the future actor Mel Ferrer. Boucher and McComas praised his 1951 collection of captioned drawings, Dance of Death, as "superlative macabre humor in a welcome modernization of a great ancient art-form.". Charlot also illustrated the book 'Springtime, Tales of the cafe Rieu' by J.B. Morton in 1956.
Selected Works 
1923,"Massacre in the Main Temple", 14 by 26, Fresco at the Antiguo Colegio de San Ildefonso.
1949,"Cargadores","Danza de los Listones", and "Lavanderas", Frescos at the Secretaria de Educación,México.
1924,"Shield of the National University of Mexico, with Eagle and Condor", 16 by 20 in., Fresco at the Biblioteca Pan-Americana, México.
1935,"Head,Crowned with Laurels", 16 by 20 in., Fresco at the Strauben-Muller Textile High School, New York.
1949,"Relation of Man and Nature in Old Hawaii", 10 by 29 ft., Fresco at the University of Hawai’i-Manoa, Honolulu, Hawaii.
1952,"Early Contacts of Hawaii with the Outer World",11 by 57 ft., Fresco at the Bishop Bank, Honolulu, Hawaii.
- Department of Education, State of Hawaii, Artists of Hawaii, Honolulu, Department of Education, State of Hawaii, 1985, pp. 15–22.
- Haar, Francis and Neogy, Prithwish, "Artists of Hawaii: Nineteen Painters and Sculptors", University of Hawaii Press, 1974, 42-49.
- Morse, Morse (ed.), Honolulu Printmakers, Honolulu, HI, Honolulu Academy of Arts, 2003, pp. 31 & 40, ISBN 0-937426-58-X
- Radford, Georgia and Warren Radford, "Sculpture in the Sun, Hawaii's Art for Open Spaces", University of Hawaii Press, 1978, 92.
- Tuck, Donald H. (1974). The Encyclopedia of Science Fiction and Fantasy. Chicago: Advent. p. 98. ISBN 0-911682-20-1.
- Yoshihara, Lisa A., Collective Visions, 1967-1997, [Hawaii] State Foundation on Culture and the Arts, Honolulu, Hawaii, 1997, 16.
- Charlot, Jean, "An Artist on Art: Collected Essays of Jean Charlot",p.4.University Press of Hawaii,Honolulu,1972,ISBN 0-87022-118-3.
- Morse, Peter, "Popular Art: The Example of Jean Charlot".Capra Press,1978,ISBN 0884960781, 9780884960782.
- The Jean Charlot Collection, University of Hawai'i at Manoa Libraries. "Murals and Sculptures by Jean Charlot"
- Charlot, Jean, "An Artist on Art: Collected Essays of Jean Charlot", p.4.University Press of Hawaii,Honolulu,1972,ISBN 0-87022-118-3.
- "Recommended Reading," F&SF, April 1952, p.95