He was born on July 25, 1839 at Saint-Étienne, Loire, and entered the French Navy, and after voyaging in Brazilian waters and the Pacific, he obtained a post on the staff of Admiral Léonard Victor Charner, who from February 1860 to November 1861 was campaigning in Cochinchina. After some time spent in France, Garnier returned to the East, and in 1862, he was appointed inspector of native affairs in Cochinchina, and entrusted with the administration of Cholon, a suburb of Saigon.