To further protect New Madrid from Union attack, a smaller fort was built on the east side of town at the mouth of St. John's Bayou. This upper fort, named Fort Bankhead (the original location was washed away by the ever-changing Mississippi River) after its artillery Captain Smith P. Bankhead, was a strong parapet behind an abates of brush and felled trees. Dirt and bags of shelled corn made a parapet ten feet thick. Known also as Fort New Madrid, it contained seven cannon mounted on wooden supports.
Fort Bankhead and its three regiments were under command of the newly arrived Colonel Lucius M. Walker, nephew of former President James Polk and a prominent Memphis businessman. His command consisted of the 5th Tennessee, 40th Tennessee, Colonel Alpheus Baker's 1st Alabama, Tennessee, Mississippi Infantry and Bankhead's Artillery.
Fort Bankhead tried to hold its own during the siege of New Madrid. Two heavy guns in the Fort became dismantled with two men wounded. After regaining their composure, the confederates began scoring some hits of their own. One of the Federal cannonballs that had landed inside Fort Bankhead, killing two mules, was reloaded and returned with devastating effect.
Fort Bankhead was never fully garrisoned or finished to the degree it needed to be and unable to hold New Madrid against the Federals' siege guns, the Confederate commanders ordered the evacuation of the gunboats and their position at the Fort in March 1862 during the night in the middle of a rainstorm with much confusion. The next morning the Federals quickly occupied New Madrid and entered the deserted fort.