In August 1861, Breckinridge joined the U.S. Army and was appointed an aide-de-camp to George H. Thomas, and served with him at Mill Springs and Shiloh. While serving at Corinth, he was commissioned a lieutenant in the 2nd US Artillery. He served in the Atlanta Campaign, and was captured following the death of James B. McPherson. After being exchanged, he served out the remainder of the war as a mustering officer, and received brevet promotions to captain (July 1864) and major (March 1865). He received promotions to the full ranks of captain and major in 1874 and 1881 respectively.