When Virginia seceded from the Union, Jackson, a proponent of slavery, resigned from his position as judge and enlisted in the Confederate States Army as a Private. Recommended to General Robert E. Lee, he quickly became an officer, then Lieutenant Colonel of the 31st Virginia Infantry Regiment. Assigned to the command of Gen. Robert S. Garnett, he participated in the Western Virginia Campaign and the battles of Rich Mountain and Cheat Mountain. In July 1861 he was promoted to rank of Colonel. In early 1862 he became a Volunteer Aide-de-camp to his cousin, Maj. Gen. Thomas J. Jackson; and participated in his campaigns during the year.