 Bramlette resigned his judgeship and accepted a commission as a colonel in the Union Army on August 7, 1861. In violation of Kentucky's agreement to remain neutral in the Civil War, he raised and commanded the 3rd Kentucky Infantry. On September 19, the 3rd Kentucky marched on Lexington to forestall a peace conference scheduled there on September 21 and to arrest the state's junior Senator, John C. Breckinridge. A delay allowed Breckinridge to escape before the arrest was made, and he enlisted in the Confederate Army shortly thereafter.
