In 1861, Polk enlisted in the Yell Rifles as a private under Patrick Cleburne, who he served under during most of the War. At the Battle of Shiloh, then Junior Second Lieutenant Polk was wounded in the face. He was promoted to colonel of the 15th Arkansas Infantry Regiment following Shiloh. When Cleburne was promoted to divisional command, Polk was appointed brigadier general to date from December 13, 1862. Polk took part in fighting at Stones River, Chickamauga, Chattanooga, and in the Atlanta Campaign. In June 1864, Polk was severely wounded (the fourth time during the war) at the Battle of Kennesaw Mountain and was honorably discharged from the Army.