Upon the approach of Confederate forces, Cooper and his new unit fled to Kentucky. He was mustered in as captain of Company A of the 1st Tennessee Infantry on August 4, 1861. He took part in operations around Cumberland Gap, and was present at the Battle of Mills Springs in January 1862. In March of the same year, Cooper's company attacked and broke through Confederate defenses at Big Creek Gap, a key mountain pass in northern Campbell County. In May 1862, Cooper was promoted to colonel and placed in command of the 6th Tennessee Infantry, which he organized and recruited. In July 1862, Cooper and his regiment attacked a Confederate force at Wallace's Crossroads (near modern Andersonville, Tennessee), killing five soldiers and capturing several others.