Colonel Hill resigned in 1863, and Captain William M. Watkins succeeded him as colonel. The regiment remained at Camp Trenton, unattached to any brigade, until just before the Battle of Shiloh, April 6-7, 1862. The action report for that engagement stated the 47th, unattached, arrived on the field April 7. Brigade, composed of the 12th, 13th, 22nd and 47th Tennessee Infantry Regiments, and Bankhead's Battery. The regiment left Corinth May 29 for Tupelo, Mississippi where it remained until July 25.
Company reports show much sickness in the regiment while at Tupelo.
It left Tupelo via Mobile, and Chattanooga, for Knoxville, to join Major General E. Kirby Smith for his invasion of Kentucky. From Knoxville, it marched on foot, many of the men barefoot, over the Cumberland Mountains to Barbourville, to London, to Richmond, Kentucky, where it was engaged in the battle on August 30, 1862. From Perryville it retreated through Harrodsburg, Kentucky, and Cumberland Gap, Tennessee, to Knoxville, where it took the railroad to Chattanooga. In this battle the 47th was commanded by Captain W. M. Watkins, and reported 86 casualties out of 263 engaged. Following this battle, the regiment retreated to Shelbyville, arriving January 14, where it was on Provost Guard duty.