Byrd fled to Kentucky in August 1861, and was mustered into the Union Army as a colonel on September 1 of that year, in command of the First Tennessee Volunteer Infantry. This unit was the first Union regiment of the war composed primarily of refugees from East Tennessee. During the first half of 1862, the First Tennessee was involved in numerous skirmishes in the Cumberland Gap area, and was present at the Battle of Mill Springs. In February 1862, Byrd suffered a wound that left him incapacitated for a month. After withdrawing northward with Union forces to the Ohio River in September 1862, the First Tennessee was reassigned to the Army of the Cumberland.