In March 1862, Patrick was appointed as a brigadier general of volunteers. His brigade was assigned to the division of Brig. Gen. Rufus King in the army of Maj. Gen. Irvin McDowell and sent to the Shenandoah Valley in northern Virginia, where Patrick's men occasionally fought against Confederates under Stonewall Jackson. He was subsequently appointed military governor of Fredericksburg, Virginia, in April 1862. Transferred later in the year to the Army of the Potomac under Maj. Gen. George B. McClellan, he commanded the 2nd Brigade, 3rd Division, I Corps in the defenses of Washington, D.C.. Patrick's brigade (renumbered as the 3rd Brigade) suffered hundreds of casualties in the Maryland Campaign, seeing action at the battles of South Mountain and Antietam.