The regiment was ordered to the mountains of West Virginia, where it performed arduous and discouraging service in the campaign on the Gauley and Cheat rivers. The regiment was engaged in the Battle of Cheat Mountain and the Battle of Greenbrier River. This was followed by hard marching under Stonewall Jackson (whom Col Rust later described as "an impracticable old schoolmaster who said grace before he ate and prayed before going to bed") in the Valley Campaign. Under General Jackson at Winchester, in January, 1862, the Third Arkansas marched to Bath and Romney, returned to Winchester, and was ordered thence to Fredericksburg and assigned to the brigade of Gen. Theophilus H. Holmes. Colonel Rust was promoted to Brigadier-General about this time, and was transferred to a command in the western armies. Van. Manning was promoted to the Colonel of the regiment succeeding Rust.