Wilson first served as a assistant topographical engineer during the Port Royal expedition of 1861 during his appointment with the Department of the South. Then, he acted as aide-de-camp in the Army of the Potomac, being present at South Mountain and at Antietam. He was transferred to the Western theater to Grant's general staff. In October 1863 Wilson was appointed brigadier general. In February 1864 he was sent to Washington to be appointed chief of the cavalry bureau. In May 1864 he returned to field duty as division commander in the Overland and Richmond campaigns under Grant. In late September, Wilson was sent again to West as he assumed the position of chief of cavalry of Sherman's Military Division of the Mississippi. He led his men through the Savannah campaign to the capture of Selma, Alabama. After the end of the war, he would receive a brevet of major general.