In early 1861, Harris organized a Mississippi militia company called the "Warren Rifles" and was captain of the company on April 25, 1861. On June 1, 1861, the company became Company C of the 19th Mississippi Infantry Regiment. The regiment soon was sent to Virginia, but did not engage in the First Battle of Bull Run or other significant action until the Battle of Williamsburg in the Peninsula Campaign. He was promoted to major on March 5, 1862. His regiment went on to fight in the Battle of Seven Pines and the Seven Days Battles. He was wounded on May 5, 1862, at the Battle of Glendale (Frayser's Farm) on June 30, 1862 and the Second Battle of Bull Run on August 30, 1862. After the Antietam Campaign, He was promoted to lieutenant colonel.