Immediately after Virginia seceded, McCausland recruited an artillery company from Rockbridge County (the 1st Rockbridge Artillery) but refused a command, instead recruiting in the Kanawha Valley at General Robert E. Lee's request. On July 16, 1861, McCausland was commissioned as a colonel and placed in command of the 36th Virginia Infantry Regiment. The regiment had been formed from the 2nd Kanawha Regiment and part of the 3rd Kanawha Regiment, which had been recruited heavily from the south-western counties of what became West Virginia during the war. McCausland's regiment fought in the brigade of Brigadier General John B. Floyd in western Virginia and was transferred to Bowling Green, Kentucky, to serve in General Albert Sidney Johnston's army. McCauland and his men fought at the Battle of Fort Donelson and escaped before the Confederates surrendered the fort in February 1862. For the remainder of 1862 and 1863, McCausland's troops fought in the Department of Southwest Virginia. There, McCausland gained the nickname "Tiger John" for his fearless partisan raids.