Missing the Gettysburg Campaign due to his injuries, Cox did not return to the field until the fall of 1863. While temporarily in command of Ramseur's Brigade because the general was on leave to get married, Cox was wounded in the face and right shoulder early in the battle of Kelly's Ford on November 7, 1863. Shipped to the hospital in Richmond, the wound resulted in a 40-day furlough to recuperate. He fought with distinction at the battles of the Wilderness and Spotsylvania Court House, being personally commended by General Robert E. Lee for bravery in fighting on May 12. Afterwards he was assigned command of a brigade of North Carolina infantry, despite being junior in rank to other colonels in the brigade. He led his troops at the Battle of Cold Harbor and then accompanied the Army of the Valley under Maj. Gen. Jubal Early in the Shenandoah Valley. At the Battle of Monocacy, Cox's brigade played a prominent role in the day-long fighting.