When Colonel John S. McCalmont resigned in May 1862, Kirk was promoted to colonel. He commanded the regiment during the battles of Beaver Dam Creek, Gaines Mill, Glendale and Second Bull Run. In the first three actions, the regiment belonged to the 3rd Brigade of the 3rd Division of Maj. Gen. Fitz-John Porter's V Corps. At Second Bull Run, it fought with the 3rd Brigade of John F. Reynolds's independent division. He briefly led the brigade before being wounded and out of action. As a result of his injuries, he missed the battles of South Mountain and Antietam. When it became evident that his wounds would prevent any further field duty, he resigned from the army on October 18, 1862.