From July 1863 to January 1864, while recovering from wounds, he served on the staff of Ohio governor David Tod and led Ohio Militia units in response to Morgan's Raid. He later commanded the 3rd Brigade of the 4th Division of the XXIII Corps in Kentucky and Tennessee and participated in Sherman's Atlanta Campaign at the battles of Rocky Face Ridge and Resaca. Runkle was honorably mustered out July 21, 1864 and on August 29, 1864, he was appointed lieutenant colonel in the Veteran Reserve Corps where he commanded the 21st Regiment until the war ended.