Sullivan helped recruit and organize a three-months' infantry regiment, the 6th Indiana Volunteers. He was elected as a captain and led his troops into combat at the Battle of Philippi in western Virginia. Following the expiration of his term of enlistment, Sullivan mustered out of the army. However, he soon received an appointment from Governor Oliver P. Morton as the colonel of the 13th Indiana, a three-years' regiment. Sullivan returned to western Virginia in the army of George B. McClellan and fought at Rich Mountain and Cheat Mountain in the summer of 1861.