At the beginning of the Civil War, Hays re-entered the service as colonel of the 63rd Pennsylvania Volunteer Infantry Regiment, also holding the rank of captain in the 16th U.S. Infantry in the regular army to date from May 14, 1861. His men knew him to be "as brave as a lion." During the Peninsula Campaign, he was attached with his regiment to the first brigade of Kearny's division of Heintzelman's III Corps. He fought in the battles of Yorktown, Williamsburg, Seven Pines, Savage's Station, and Malvern Hill. At the close of the Seven Days Battles, he was appointed a brevet lieutenant colonel in the regular army for gallantry in action, as Hays had directed a bayonet charge with his regiment into the enemy lines to cover the retreat of his brigade. Hays briefly went on sick leave a month later, suffering from partial blindness and paralysis of his left arm, injuries incurred from battle.