When the Civil War broke out, Kirkland was initially appointed a captain in the Confederate army and then elected colonel of the 11th North Carolina Volunteers, later designated the 21st North Carolina, in June 1861. He commanded his regiment at First Manassas as part of Brig. Gen Milledge Bonham's brigade, but was not significantly engaged. In October, the 21st North Carolina was attached to Isaac Trimble's brigade and the following spring, he participated in Stonewall Jackson's Shenandoah Valley Campaign. Kirkland was shot through both thighs during the First Battle of Winchester, putting him out of action for several months. During his recuperation, Kirkland served as chief of staff for Patrick Cleburne during the Murfreesboro campaign in December 1862.