Canguilhem entered the École Normale Supérieure in 1924 as part of a class that included Jean-Paul Sartre, Raymond Aron and Paul Nizan. He aggregated in 1927 and then taught in lycées throughout France, taking up the study of medicine while teaching in Toulouse.

He took up a post at the Clermont-Ferrand based University of Strasbourg in 1941, and received his medical doctorate in 1943, in the middle of World War II. Using the pseudonym “Lafont” Canguilhem became active in the French Resistance, serving as a doctor in Auvergne.

Canguilhem’s principal work in philosophy of science is presented in two books, Le Normal et le pathologique, first published in 1943 and then expanded in 1968, and La Connaissance de la vie (1952). Le Normal et le pathologique is an extended exploration into the nature and meaning of normality in medicine and biology, the production and institutionalization of medical knowledge. It is still a seminal work in medical anthropology and the history of ideas, and is widely influential in part thanks to Canguilhem’s influence on Michel Foucault. La Connaissance de la vie is an extended study of the specificity of biology as a science, the historical and conceptual significance of vitalism, and the possibility of conceiving organisms not on the basis of mechanical and technical models that would reduce the organism to a machine, but rather on the basis of the organism’s relation to the milieu in which it lives, its successful survival in this milieu, and its status as something greater than “the sum of its parts.” Canguilhem argued strongly for these positions, criticising 18th and 19th century vitalism (and its politics) but also cautioning against the reduction of biology to a “physical science.” He believed such a reduction deprived biology of a proper field of study, ideologically transforming living beings into mechanical structures serving a chemical/physical equilibrium that cannot account for the particularity of organisms or for the complexity of life. He furthered and altered these critiques in a later book, Ideology and Rationality in the History of the Life Sciences.

By 1948 he was the French equivalent of department chair in philosophy at Strasbourg as well. Seven years later, he was named a professor at the Sorbonne and succeeded Gaston Bachelard as the director of the Institut d’histoire des sciences, a post he occupied until 1971, at which time he undertook an active emeritus career.

In 1983 he was awarded the Sarton Medal by the History of Science Society. In 1987 he received the médaille d’or, awarded by the Centre national de la recherche scientifique (CNRS).