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. His great grandfather had immigrated to Mexico in the 1820s shortly after the country's independence from Spain and married a woman who was half Aztec. This was likely the source of a myth which developed around Charlot casting him as a descendant of Aztec royalty.
From an early age Charlot was fascinated with the Mexican manuscripts and art in the collection of his Great Uncle Eugene, and by the pre-Columbian artefacts of a neighbor and family friend, Désiré Charnay, who was a well-known archaeologist. As a teenager he began learning the Aztec language, Nahuatl. He studied art in Paris before serving in the French Army during World War I. In 1920, his scale drawings for the mural decorations of a church were included in an exhibition of religious art at the Louvre.
Charlot spent an extensive period of his life living and working in Mexico. In 1921, after his father died, he and his mother left Europe to settle in Mexico City. He met Fernando Leal (1896–1964) and shared his studio with him. Charlot was deemed "a fine person who is doing important work" by Diego Rivera, the renowned Mexican painter and muralist. Rivera introduced Charlot to other young artists, such as Pablo O'Higgins (born Paul Stevenson Higgins and who came to live in Mexico in 1924, having grown up in Salt Lake City, Utah). O'Higgins would later recall that he met Charlot at the former's studio, when he was painting a nude of Luz Jimenez, a very beautiful Mexican Indian woman model to Diego Rivera. Luz's native language was nahuatl, which she taught to Charlot as she posed for him. Charlot and O'Higgins shared an interest in learning about Mexico and traveled together exploring the country, sometimes with Anita Brenner, a Jewish 19-year-old at that time with whom Charlot seemed in love and collaborated in several literary and illustration projects.
Charlot married a close friend of O'Higgins, Dorothy Day, an artist who had also grown up in Salt Lake City. Her family was Mormon but later left the church. Her dark skin and brown eyes had long left her feeling uncomfortable in blond, blue-eyed Salt Lake society; she recalled that one day some American Indians came to her door and she saw people who looked like herself for the first time, and connected with them. At age twenty, Dorothy had changed her name to Zohmah and traveled to Mexico. She got involved in the Mexican art movement of the 1920s and 30s, and became close friends with young Mexican and American artists, such as Charlot and O'Higgins, in the circle of Mexican muralist Diego Rivera.
Charlot and O'Higgins had a long-lasting friendship, sharing their interest on each other's work even after Charlot went with his mother to live in New York in 1928. When in Mexico City, Charlot would stay in a humble room Pablo rented in downtown Mexico City on the roof of a dilapidated building on the street of Belisario Dominguez. In December 1930, to prepare for his solo exhibit in early 1931 at the John Levy Gallery in New York, O'Higgins lived with Charlot for six months in his small unheated apartment on Union Square and 14th Street, near the Art Students League, where Charlot was teaching. At the same time, mid-January 1931, a few blocks away, José Clemente Orozco was painting murals for The New School at 66 West 12th Street. Charlot and Orozco had maintained frequent correspondence in previous years.
Both commented on each other's murals in Hawaii in 1952.
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.
Jean Charlot is generally recognized as having brought international attention to José Guadalupe Posada, a Mexican printer who had produced more than 15 thousand prints and lithographs, devoted mostly to the popular readers of newspapers in pre-revolutionary Mexico, in which he would present political satires using cartoon-like skeletons. The original style and plastic language of Posada's art struck Charlot when he saw his prints being sold in 1922 on street corners, and he went on to find his forgotten printing blocks (woodcuts, leadcuts, zinccuts, etc.) in the workshop of Posada's former publisher. With O'Higgins and the son of Posada's publisher, Charlot participated in 1928 and 1930 in the publication of catalogues of Posada's prints, a project conceived by Frances Toor which piqued public interest in Posada. Posada's skeletons and skulls, rooted in pre-Hispanic religious ritual, were later adapted by Rivera, Frida Kahlo, O'Higgins, and many others, and are now icons acknowledged worldwide as being at the heart of Mexican popular art and handcrafts. Jean Charlot himself was much interested in and also started avant-garde woodcut.
After the Mexican Revolution (1910-1917), post-revolutionary governments sought to educate the public on the principles of social justice, as consecrated in the new constitution. Mural painting became an extraordinary visual vehicle, for occupying public spaces like government buildings, schools and markets where it was accessible to all people and spoke even to the illiterate, in contrast to traditional easel painting aimed at private art consumption by the educated. During the government of President Alvaro Obregon (1921-1924) mural painting was actively promoted by Minister of Education Jose Vasconcelos. Diego Rivera's strong personality and political connections led to many important early commissions. His first commission from Vasconcelos was to paint a mural in the Preparatory School, where four young artists dared to accept Vasconcelos' challenge. Jean Charlot was one of them, and also his friend and roommate Fernando Leal who invited him to get involved. Actually, Charlot's fresco "Massacre in the Templo Mayor" (1921–1922) is in front of Fernando Leal's "The Dancers of Chalma" (1921–23). In his fresco Charlot portrayed himself, Leal and Diego Rivera. Charlot's was the first mural finished and the first in the fresco technique. Thus, Charlot participated in the founding of Mexican muralism.
The next project Rivera took on was in the Court of Labor at the Ministry of Education building; other young artists, including Charlot, Xavier Guerrero, and Amado de la Cueva, were assigned walls in the Court of Fiestas in the same building. Charlot considered it a first attempt at "communal painting". Rivera, however, eventually wrested control of the project, acquiring more space for himself and recasting the other artists in the role of assistants, even painting over one of Charlot's finished murals, Danza de los Listones (Dance of the Ribbons) to create room for his own Market Place. According to John Charlot, son of Jean, in the beginning only younger artists dared to undertake commissions for large mural paintings. While Vasconcelos himself preferred non-political allegorical works, he carefully avoided guiding the artists, who increasingly became more political in reflecting the ideas of the revolution.
In 1928, works by Charlot were included with those of 21 other artists (including Rivera, Orozco, O'Higgins, Siqueiros, and Carlos Mérida) in an exhibition at the Art Center Gallery in New York organized by Frances Flynn Paine, the manager of a Rockefeller fund to sponsor Mexican artists. The exhibition had the co-sponsorship of the Mexican Ministry of Education and the Mexican National University.
Between 1926 and 1928 Charlot spent three seasons deeply immersed in the excavation of Mayan temples at Chichen Itza. Hired by Sylvanus Morley of the Carnegie Institution and under the field direction of Earl H. Morris, Charlot meticulously traced and copied bas-reliefs and painted surfaces as they were unearthed, creating an invaluable guide to the reconstruction of some of the key structures of the temple complex. The work had a major influence on his own art, and led to a long friendship with Earl Morris and his wife Ann, a fellow painter-copyist at Chichen Itza. The Morrises took care of Charlot after his mother died in New York City in the winter of 1929, and together the three co-authored The Temple of the Warriors at Chichén Itzá, Yucatan, published in two volumes in 1931 and considered a classic in its field
In the U.S., Charlot executed commissions for the Work Projects Administration's Federal Arts Project, including the creation of murals for Straubenmuller Textile High School in Manhattan during 1934–1935, and, in 1942, an oil on canvas mural for the post office in McDonough, Georgia titled Cotton Gin, 4.5 ft × 11 ft (1.4 m × 3.4 m).
Charlot went to Colorado Springs, Colorado in 1947 to take a job at the Colorado Springs Fine Arts Center, where 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. There, he developed a close friendship with the world-famous local artist Madge Tennent and collaborated with Juliette May Fraser, an accomplished muralist in her own right, on several major commissions in and around Honolulu. During the summer of 1969, Charlot worked with Tony Smith at UH and Smith thanked him by creating a piece in the For... series named 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 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.
In 1972, Charlot published "An Artist on Art: Collected Essays of Jean Charlot", which discussed Mexican art history
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.