On February 7, 1831, Huger married a cousin named Elizabeth Celestine Pinckney. They would have five children together; Benjamin, Eustis, Francis, Thomas Pinckney and Celestine Pinckney. One of his sons, Francis (Frank) Kinloch Huger, also attended West Point and graduated in 1860. Frank Huger would enter the Confederate forces during the American Civil War as well, rising to the rank of lieutenant colonel and leading a battalion of field artillery by the end of the conflict. On May 30, 1832, Huger was transferred to the Army's ordnance department with the rank of captain; he would spend the rest of his U.S. Army career with this branch. From 1839 to 1846 he served as a member of the U.S. Army Ordnance Board, and from 1840 into 1841 he was on official duty in Europe. Huger again commanded the Fort Monroe Arsenal from 1841 to 1846, until hostilities began with Mexico.