In 1861 Hindman was commissioned as a colonel in the 2nd Arkansas Infantry. In September, he was promoted to brigadier general. He temporarily commanded the Trans-Mississippi Department before he was relieved to take a field command. He served in the Battle of Prairie Grove, and later in the battles of Chickamauga and Chattanooga. He was severely wounded in the Atlanta campaign. He was forced to limit himself to administrative duties for the rest of the war.
