In 1863 at the Battle of Stones River, Johnson commanded a division on the right flank under Major General Alexander McCook. Johnson's command was flanked from its position by the initial Confederate attack. At the Battle of Chickamauga, his division of the XX Corps formed part of the command of Maj. Gen. George Henry Thomas on the Union left. During the Battle of Chattanooga, his division was one of the several that charged up Missionary Ridge. The next year he commanded a division in the Army of the Cumberland during the invasion of Georgia and was severely wounded at the Battle of New Hope Church on May 28, 1864.