During the Northern Virginia Campaign, Rooney played a leading role in Stuart's well-crafted attack on General John Pope's supply base at Catlett's Station on August 22, 1862, capturing a paymaster's safe full of Yankee greenbacks. His cavalry regiment was assigned to the brigade of Brig. Gen. Fitzhugh Lee, his cousin, for the Maryland Campaign. Following the Battle of South Mountain, Lee was knocked unconscious after a horse fell from under him, and was unable to participate in the Battle of Antietam. Upon his recovery, he temporarily commanded Fitzhugh Lee's cavalry brigade in Stuart's Chambersburg Raid; his conduct earning him promotion to Brigadier General. He then commanded the 3rd Brigade of Stuart's Cavalry Division at the Battles of Fredericksburg mere weeks after the death of his infant daughter. During the Battle of Chancellorsville the following year, Lee was detached from Stuart's cavalry to defend against Stoneman's 1863 Raid.