Palmer fought primarily in the Western Theater of the American Civil War. He was part of the garrison surrendered at Fort Donelson on February 15, 1862, and was exchanged on August 15. That October Palmer was given brigade command in the Army of Mississippi. He fought in the Battle of Stones River and was wounded in his right shoulder and his right leg on January 2, 1863. Palmer fought during the Battle of Chickamauga that fall, and was wounded on September 19 when he again hit in his right shoulder.