Kautz was a captain with the 6th U.S. Cavalry during the Peninsula Campaign from April to July 1862. Transferred to the Western Theater, Kautz later assisted in operations as a colonel with the 2nd Ohio Cavalry against Confederate General John Hunt Morgan's raid behind Union lines in Indiana and Ohio during June–July 1863 and under the command of Maj. Gen. Ambrose Burnside at the Battle of Knoxville from September to December 1863.