Cooper served as U.S. Indian agent in Oklahoma prior to the war. In 1861, he was recruited by the Confederate government to gain the allegiance of the Indians. He was commissioned a colonel of the First Choctaw and Chickasaw Mounted Rifles and was promoted to brigadier general in 1863. He commanded the Indian brigade during the second invasion of Missouri by General Sterling Price. After the war, he prosecuted the claims of the Indians against the U.S. government.