After the Seven Days Battles, Huger was assigned to be assistant Inspector General of artillery and ordnance for the Army of Northern Virginia. He held this post from his relief on June 12 until August, when he was sent to the Confederate Trans-Mississippi Department. Considered too old for field command, he would spend the remainder of the war in administrative duties. Huger was made the department's inspector of artillery and ordnance on August 26, and then was promoted to command of all ordnance within the department in July 1863. This position he held until the end of the American Civil War in 1865, when he surrendered along with Gen. Edmund Kirby Smith and the rest of the Confederate Trans-Mississippi forces. Huger was paroled from Shreveport, Louisiana, on June 12 of that same year and returned to civilian life.