Josef Šíma was born in 1891 into a family of artists: his grandfather was a sculptor and stonemason, his father a professor of drawing. In 1909 he studied at the Academy of Arts, Architecture and Design in Prague and from 1910 to 1914 at the Academy of Fine Arts in Prague under Professor Jan Preisler and Vlaho Bukovac. From 1913 to 1915 he also studied civil engineering in Brno.

He actively participated in combat during World War I (1915–1918). After his return he chaired the Aleš Association of Fine Artists in Brno. In 1920, while starting to work as an assistant of technical drawing at the Brno University of Technology, he also co-founded the avant-garde Devětsil group. His last work in Prague was a stage set for a production of Karel Čapek’s R.U.R.

Prior to his departure for Paris in 1920, Šíma spent nine months in the Basque town of Hendaye, working as a painter for the renowned stained glass manufacturer Mauméjean. While he acquired French citizenship in 1926 following his marriage to Nadine Germain in 1923, he remained in active contact with his former homeland. His exhibitions, relating his impressions of Paris, were held primarily in cooperation with the Otakar Štorch-Marien's publishing house Aventinum in Prague. Aventinum also published his most significant graphic album entitled Paris, a collection of eighteen hand-coloured etchings presented alongside Paris-themed texts by various French writers, a work considered iconic within the Czech-French artistic milieu.

Throughout the 1920s, Šíma made a living illustrating the works of his Parisian poet friends. However, from the very beginning he also focused on his own paintings, producing primarily dream landscapes and portraits. While his first exhibition, held in 1929, featured mainly landscapes, L’énigme de la face, held in 1930, included primarily portraits of his friends. Both exhibitions were held at the Povolozki Gallery at 13, rue Bonaparte. The preface to the second exhibition catalogue was written by poet Roger Gilbert-Lecomte, like Šíma himself a member of the Le Grand Jeu (1927–1932) group, which tended to gravitate toward imaginative surrealism, i.e. a form unlike Breton’s surrealism, previously defined as art of an unconscious nature. Although relations between the two groups escalated somewhat in 1929, Šíma managed to maintain good relations with both Breton and Éluard, even accompanying them on their famous visit to Prague in 1935. Though subject to the 1939 mobilisation, he was subsequently retired from the military by December. Suffering from great mental anguish, Šíma spent the war years in southern France, where he also became involved in the resistance movement; unfortunately, he stopped painting entirely. After the war he was appointed government commissioner for cultural affairs at the restored Czechoslovak embassy in Paris, located in Masaryk’s house in the rue Bonaparte. As commissioner, he organized an exhibition of Czech artists in France in 1945, and in 1946 travelled to Prague with Paul Éluard to select works for an exhibition of new Czechoslovak art, held in the summer of that year at the La Boétie Gallery. In Czechoslovakia, he befriended members of Group 42, including Jiří Kolář. After 1948, he never visited his former homeland. In 1950, for obvious political reasons, he resigned the post of embassy commissioner for cultural relations and returned to painting. He was fortunate to be represented by significant gallerists, initially by Paul Facchetti and, since 1965, by Jean Hugues, owner of the renowned Le Point Cardinal Gallery. A leading mediator of the literary and visual arts world, Hugues introduced Šíma to an outstanding circle of poets and painters, including René Char and Henri Michaux. While staying in Reims (1963–1969), Šíma revisited his first French profession and created stained-glass windows for the local St. Jacques Church at Charles Marq’s famous glassworks. Though marred by the tragic outcome of the suppressed Prague Spring, an exhibition held at the Musée national d’art moderne in Paris from 7 November to 23 December 1968, i.e. three years before Šíma's death, comprised a dignified appreciation of the painter’s life work. His last significant Paris exhibition took place in 1992.