Magendie was a faculty at the College of France, holding the Chair of Medicine from 1830 to 1855 (he was succeeded by Claude Bernard, who worked previously as his assistant).

In 1816 he published Précis élementaire de Physiologie which described an experiment first illustrating the concept of empty calories:[1] His most important contribution to science was also his most disputed.

Contemporaneous to Sir Charles Bell, Magendie conducted a number of experiments on the nervous system, in particular verifying the differentiation between sensory and motor nerves in the spinal cord, the so-called Bell–Magendie law.

Magendie was also a notorious vivisector, shocking even many of his contemporaries with the live dissections that he performed at public lectures in physiology.

A Quaker once visited him, questioning him about vivisection; according to Anne Fagot-Largeault's inaugural lesson at the College of France, he responded with much patience, argumenting the reasons of animal experimentation.