Flourens, who was born at Maureilhan in France, studied medicine at the University of Montpellier, graduating in 1813. Moving to Paris he was fortunate enough to be taken in hand by the powerful Georges Cuvier, serving as his deputy at the Collège de France from 1828. After Cuvier's death in 1832, Flourens succeeded him as professor of anatomy and secretary of the Académie des Sciences.

In 1824 Flourens published his highly influential Recherches expérimentales sur les propriétés et les fonctions du système nerveux dans les animaux vertébrés (Experimental Researches on the Properties and Functions of the Nervous System in Vertebrates) in which he demonstrated the main roles of different parts of the central nervous system. Extending the work of the Italian anatomist Luigi Rolando on the nervous system, Flourens removed various parts of the brain and carefully observed the resulting changes. Thus he found that removal of the cerebral hemispheres of a pigeon destroyed the sense of perception. Removal of the cerebellum destroyed coordination and equilibrium and excision of the medulla oblongata caused respiration to cease. He also exposed the spinal cord of a dog from head to tail and found that while stimulation lower down would produce movement there came a point higher up where no muscular reaction could be elicited. Flourens is also known for important work on the semicircular canals in the ear, demonstrating their function in balance.

Although Flourens assigned different roles to different anatomical parts of the brain he was not prepared to go further and localize different roles and powers within each part. It was not until 1870 that Gustav Fritsch and Eduard Hitzig were able to break this unitary picture and establish cerebral localization experimentally.

Flourens is also remembered for his attack on Darwin in his Examen du livre de M. Darwin (1864; Examination of Mr. Darwin's Book) in which he poured scorn on Darwin's “childish and out of date personifications.”