On October 5, 1861, the Gainsville Volunteers were transferred to the service of the Confederate States of America as the 3rd Regiment, Mississippi Volunteers. This took place at Camp Clark, Shieldsboro (now Bay St. Louis), Mississippi, by the authority of Brigadier General Charles M. Dahlgren who commanded the 3rd Brigade of the Army of Mississippi. On that date, David Stockstill was elected 3rd Lieutenant.

In the latter part of November, General Lovell called the 3rd Regiment in from the Mississippi Sound, and sent it, 800 strong, to the aid of General Polk at Columbus, Kentucky. This was protested against by Mississippi Governor Pettus and Confederate President Davis. Consequently, General Lovell secured the return of the 3rd Regiment in January, 1862, as "a regiment peculiarly adapted to, and indeed, raised mainly for the defense of the intricate coast of Mississippi Sound."

On May 12, 1862, the regiment was re-enlisted for the war and reorganized in camp at Tangipahoa, Louisiana. On May 1, 1862, DAVID STOCKSTILL was elected 2nd Lieutenant of Company G, 3rd Regiment of Mississippi Infantry.

On May 29, 1862, General Lovell, at Camp Moore, Louisiana, sent the Third Regiment, under Colonel Mellon, to reinforce General M. L. Smith at Vicksburg. They were on picket duty during the bombardment of May 20 to July 27, 1862. They began the work of fortifying Sugar Loaf Hill and remained on the river front guarding against surprise and always ready to meet an attack.

Listed on the muster roll for July, 1862, were 35 officers and 476 men present for duty, aggregate present 709. David Stockstill was sick for 10 days during July. He was sick for the entire month of August, 1862. From his duty station at Haines Bluff near Vicksburg, Mississippi, David Warden Stockstill tendered his resignation as a 2nd Lieutenant in Company G, 3rd Regiment of Mississippi Infantry on September 28, 1862 due to ill health. His request was endorsed by the Regimental Surgeon, J. M. Bogle, and approved by the Confederate Secretary of War on October 22, 1862.

David Warden Stockstill died on August 21, 1913, in Picayune Mississippi. He was buried the next day in the New Palistine Cemetery in Picayune. He was married to Telitha Margaret Mitchell.