Returning to Arkansas, Rust received a commission as colonel on July 5, 1861, and assisted Van H. Manning in recruiting and organizing the 3d Arkansas Infantry Regiment. The Third Arkansas would become Arkansas's most celebrated Civil War regiment and the only Arkansas regiment to be permanently assigned to General Robert E. Lee's Army of Northern Virginia. In the fall of 1861, Rust and the Third Arkansas traveled to Western Virginia and took part in the Battle of Cheat Mountain under Lee. During that winter, he and the regiment were under the command of General Stonewall Jackson. They would go on to serve in almost every major battle fought in the east, including the Battle of Gettysburg, although mostly after Rust's promotion and transfer from the regiment.