By the Maryland Campaign in September 1862, he had become the colonel of the 63rd New York Volunteer Infantry Regiment in "The Irish Brigade". During the fighting around the Sunken Road at Antietam General Thomas F. Meagher, commander of the Irish Brigade, was wounded. Colonel Burke assumed command of the brigade and led it from September 17–18 when General Meagher returned to command.[2]
Burke died in Oswego at the age of 75 and was buried in the town's cemetery.