When the Southern states began seceding from the Union, Duncan reentered military service for the Confederate States of America. He enlisted in the CSA forces as a colonel of the 1st Louisiana Regular Artillery Regiment and rose in rank and status rather quickly. Promoted to brigadier general of Louisiana troops on January 7, 1862, he was assigned to command the defenses of New Orleans and the Lower Mississippi. He quickly became widely known as one of the finest artillerists in that region. He commanded Forts Jackson and St. Philip at the time of their capture by Flag Officer David Farragut on April 25, 1862. He was taken prisoner. After being exchanged, Duncan was assigned to the staff of General Braxton Bragg, becoming Chief of Staff.