During the Civil War, Pitcher participated in the defense of Harpers Ferry in June 1862, where he and his men were among the thousands of Union soldiers who surrendered to Stonewall Jackson. After being released and exchanged, he served in the Virginia campaign until the battle of Cedar Mountain (August 9, 1862), where he was severely wounded. He was then brevetted major in the regular army, and three months later was commissioned brigadier general of volunteers, but saw no further active service. On March 13, 1865, he was brevetted lieutenant colonel, colonel, and brigadier general in the regular army.