At the beginning of the American Civil War in 1861, Parker joined the Home Guard and became a first lieutenant for Company C, 6th Missouri Militia. After several months, Parker transferred from state to federal service and became part of Company H, 32nd Missouri Volunteer Infantry where he served under General William T. Sherman. During the war he saw action during the Battle of Arkansas Post, the Siege of Vicksburg, the Chattanooga Campaign, and the Atlanta Campaign. Despite participating in multiple battles, Parker was not wounded during the war. Following the capture of Atlanta, Parker's regiment began mustering out excess officers. He was promoted to captain in July 1864 and discharge from the Union Army before the end of the year.