Enlisting in the Confederate Army in April 1861, Kennedy became captain of Company E, 2nd South Carolina Infantry Regiment, under fellow Camden resident Col. Joseph Brevard Kershaw. At the First Battle of Manassas, he was struck by a Minie ball and badly wounded. Recovering, he was promoted to colonel when Kershaw was promoted to brigadier general. Kennedy's first action in command of a regiment occurred at a skirmish on the Nine-Mile Road near Richmond, Virginia, in June 1862 during the Peninsula Campaign. After fighting at the Battle of Savage's Station, he was disabled for several weeks by fever. He returned to his regiment in time for the Maryland Campaign. During Stonewall Jackson's investment of Harpers Ferry, Kennedy was with Kershaw's brigade in the capture of the important Maryland Heights. He led his regiment in Kershaw's counterattack during the Battle of Antietam, driving a part of the Union II Corps before him. However, he fell painfully wounded in the first charge, struck in the instep and Achilles tendon while crossing a wooden fence along the Hagerstown Pike. Once again recovering in time for a major battle, Kennedy led the 2nd and 8th South Carolina to the support of Gen. Howell Cobb at Marye's Heights, the focus of the hottest fighting at Fredericksburg.