In 1861, Duncan was commissioned as a colonel of artillery and was put in command of the coastal defenses of New Orleans, including Fort Jackson and Fort St.Philip. In January 1862 he received a promotion to brigadier general as he took command of the coastal defenses of Alabama, Mississippi and Louisiana. When his reserves were moved north to supplement the Confederate forces in Tennessee, he was left with inadequate defenses. He was forced to surrender to a Union fleet in April 1862. He was captured and later exchanged in August 1862. Upon his return, he become chief of staff to Gen. Braxton Bragg; however, he died of typhoid fever at Knoxville in December 1862.
