Responding to President Abraham Lincoln's call to arms at the outbreak of the Civil War, Ward recruited the 38th New York Infantry and was appointed its first colonel. He led his regiment at the July 1861 First Battle of Bull Run, becoming acting commander of Brig. Gen. Orlando B. Willcox's brigade when the latter was wounded in battle. He next saw action in the 1862 Peninsula Campaign in Brig. Gen. David B. Birney's brigade of III Corps. Ward continued to perform well during the Northern Virginia Campaign, seeing more action at Second Bull Run and Chantilly. For his efforts, he was promoted to brigadier general of volunteers on October 4, 1862, and assigned command of what had been Birney's brigade in the III Corps of the Army of the Potomac. (Birney had succeeded Maj. Gen. Philip Kearny, who had been killed leading his division at Chantilly.) Ward commanded the brigade at Fredericksburg and Chancellorsville.