Mouton was born in Opelousas, Louisiana, the son of former Governor of Louisiana Alexandre Mouton. Alfred enrolled in St. Charles College in Grand Coteau, Louisiana. Upon his graduation from St. Charles College, Alexandre Mouton secured for Alfred an appointment to the United States Military Academy in West Point, New York. Alfred was hesitant to go at first because up until that point in his life he had been only around French-speaking people and customs; he knew little English and was not accustomed to speaking it. However, his father was adamant, and he was enrolled in 1846.