His uncle, Dr. William Maffitt, adopted him at age five, and John moved to Ellerslie, outside Fayetteville, Cumberland County. By the time he was thirteen, Maffitt had a commission as midshipman in the United States Navy. He held various positions, including the command of several ships. In 1842 the navy assigned him to the United States Coast Survey. The superintendent of the survey said that, as a surveying officer, Maffitt had "not been excelled by any one with whom I have come in contact." Maffitt spent fourteen years mapping and charting coastal areas, plotting depths, locating shoals and sandbars, and determining the velocity of currents-learning many skills that would serve him well in his future career commanding blockade-runners for the Confederacy.
Upon the outbreak of war, John Newland Maffitt resigned from the United States Navy. He assumed command first of the blockade-runner Cecile and then of the gunboat CSS Florida. Maffitt could not begin attacking Union vessels with the Florida, however, because its guns were inoperable, and yellow fever incapacitated its crew. Maffitt's stepson died from the fever, and Maffitt himself was unconscious for several days. After his recovery, Maffitt sailed for the Confederate port at Mobile. Four Federal ships blockaded the harbor, but on September 3, 1862, Maffitt charged straight into the port at full steam. He later wrote, "The loud explosions, roar of shot, crashing spars and rigging, mingling with the moans of the sick and wounded, instead of intimidating, only increased our determination to enter the destined harbor." Maffitt cleverly steered straight toward the Federal ship Oneida, which backed up to avoid a collision, giving the Florida "a momentary advantage." He also maneuvered the Florida between two Union gunboats, forcing them to cease fire temporarily in order to avoid shelling each other. Thus the Florida slipped into Mobile Bay in one of the most daring naval exploits of the war. The Florida had orders to "cruise at discretion," doing "the enemy's commerce the greatest injury in the shortest time." As captain of the Florida, Maffitt carried out these instructions admirably, capturing twenty-four ships.
After a stint as commander of the CSS Albemarle in Plymouth in 1864, John Newland Maffitt accepted his last position in the Confederate navy, commander of the blockade-runner Owl, on September 9, 1864. When the war ended, Maffitt refused to surrender the ship to Federal authorities and instead sailed to Britain to relinquish command. During his Confederate service, Maffitt captured and destroyed more than seventy ships, with cargoes valued at between $10 million and $15 million. Maffitt apparently had no desire to go back to a defeated South and so remained in England. However, in 1868 he returned to North Carolina and settled on a farm he called the Moorings, located on the sound at Wrightsville Beach, New Hanover County. He married his third wife, Emma Martin, in Wilmington on November 23, 1870. The couple had three children, Mary Read, Clarence Dudly, and Robert Strange Maffitt. Emma helped her husband write several magazine articles and a novel entitled Nautilus; or, Cruising under Canvas. Published in 1871, it described three years of Maffitt's early life in the United States Navy. Maffitt died of liver disease on May 15, 1886, and was buried in Wilmington's Oakdale Cemetery