Milne-Edwards obtained a medical degree in 1859 and became assistant to his father at the Jardin des Plantes. He became professor of ornithology at the Muséum National d'Histoire Naturelle in 1876, devoting himself especially to fossil birds and deep-sea exploration. In 1881, he undertook with Léopold de Folin a survey of the Gulf of Gascony and worked aboard the 'Travailleur' and the 'Talisman' to trips to the Canaries, the Cape Verde Islands and the Azores. For this he received a gold medal of the Royal Geographical Society. He became Director of the museum in 1891.
His major ornithological works include Recherches Anatomiques et Paleontologiques pour servir a l'Histoire des Oiseaux Fossiles de la France published in two parts in 1867 and 1872, Recherches sur la Faune ornithologique etiente des iles Mascareignes et de Madagascar 1866-1874 and Recherches pour servir à l’histoire naturelle des mammifères 1868-1874. His study of fossils led to the discovery of tropical birds such as trogons and parrots from prehistoric France.
He worked with Alfred Grandidier on L'Histoire politique, physique et naturelle de Madagascar 1890-1942.