In 1863 he became a health specialist in Alexandria, then in 1875 was appointed director of the Cairo medical school.In addition to his medical duties, he conducted botanical, zoological, geological and archaeological research in Egypt and the Middle East.
The snail genus Gaillardotia (Bourguignat, 1877; family Neritidae) honors his name, as do species with epithet of gaillardotii, an example being Echinops gaillardotii (Gaillardot's globe-thistle).
His Herbier de Syrie became part of the "Herbarium Haussknecht", now located at the University of Jena.