With the secession of eleven Southern states and the outbreak of the Civil War, Miller joined the Union Army. On August 27, 1861, Governor Oliver P. Morton commissioned Miller as Colonel of the 29th Indiana Infantry. After training, the regiment was assigned to Kirk's Brigade in Alexander M. McCook's division in Buell's Army of the Ohio and marched to Tennessee. Miller saw action on the second day of the Battle of Shiloh, as well as during the subsequent Siege of Corinth. Miller led his regiment through northern Alabama and Tennessee and pursued Braxton Bragg through Kentucky. Miller commanded a brigade under James Negley during the Battle of Stones River in late December 1862. On the second day of the battle, Miller spearheaded the Federal counterattack across Stones River which repulsed John C. Breckinridge's Confederate attack. During this charge Miller was wounded in the neck.