John J. McCook was born in Carrollton, Ohio, to family patriarch Daniel McCook. He was named for his uncle, John James McCook. He enrolled in Kenyon College, but left school after completing his freshman year to enlist as a private in the 52nd Ohio Infantry on August 12, 1862, but was not mustered into the service, initially because of his age. He accompanied the regiment as a volunteer aide-de-camp. On September 12 of that year, he was commissioned as a first lieutenant in the 6th Ohio Cavalry and assigned to the staff of Major General Thomas L. Crittenden in what later became the XXI Corps in the Army of the Cumberland. McCook was involved in several campaigns and battles in the Western Theater, including Perryville, Stones River, the Tullahoma Campaign, Chattanooga, and Chickamauga.