In the spring of 1862 Wise and his stepmother moved in with relatives in Franklin County, and then in September he entered the Virginia Military Institute. He was present at the funeral of Stonewall Jackson in 1863 and was wounded but not seriously at the Battle of New Market on May 15, 1864. With the sponsorship of his father’s friend, Confederate general William Mahone, Wise received a commission in September as a drillmaster with the rank of 2nd lt. in the Confederate army. He served in southwestern Virginia, in Richmond, and at the end of the war as a courier carrying messages between Genera Robert E Lee and Confederate president Jefferson Davis. Wise was paroled late in April 1865 after General Joseph Johnston surrendered in North Carolina. Two months later, while visiting his uncle, General George Gordon Meade, in Philadelphia, he witnessed the triumphal return parade of the U.S. Army.