The son of , he was born in Versailles and studied biology and natural history at the University of Paris. In 1880, he was named deputy head assigned to organize the French exhibit at the Melbourne International Exhibition (1880). He stayed in Australia for 18 months, travelling the continent and identifying new animal species. In 1886, Boutan was named maître de conférences at the University of Lille. In the same year, he learned how to dive. In 1893, he was named professor at the Laboratoire Arago. During that year, with his brother , he developed equipment for underwater photography. In an article in The Century Illustrated Monthly Magazine, he described his apparatus; the article included an illustration of one of his cameras and several underwater images. Boutan developed a flash bulb that could be used underwater. He later used carbon arc lights for illumination.