Robert enlisted with the Confederate Army for the Civil War. He moved briefly to Missouri, where he was ordained in 1863, and served as a minister to several churches. Robert returned to Boone County, Kentucky in 1864. He routinely preached at Middle Creek, East Bend and Sand Run Baptist churches, and worked in the North Bend Association of Baptists for many years.
Robert E. Kirtley died 31 August 1898, after a long illness.