Born in Newport, Rhode Island, Decatur was a merchant captain before the Revolution. He married Ann Pine; in addition to Stephen Jr., they had two other children: Lieutenant James Decatur, who was killed in action in 1804 during the Barbary Wars, and Ann Decatur McKnight.
With the outbreak of the Quasi War with France, Decatur was commissioned as a captain in the United States Navy on May 11, 1798.
On May 5, 1798, Decatur was placed in command of the converted merchant ship USS Delaware and sailed in the first American Navy squadron to cross the Atlantic along with his son Stephen Decatur Jr.[2][3]Delawarecaptured a French privateer, La Croyable, off Great Egg Harbor, N.J., on 7 July 1798. The U.S. Navy purchased La Croyable on 30 July 1798, and renamed her USS Retaliation.[4] From 14 July to 23 September, Delaware cruised in the West Indies, often in company with the frigate USS United States, and together the ships took two privateers prize. During her second cruise in the West Indies, between 15 December 1798 and 20 May 1799, she took another prize.[3]
In accordance with the Peace Establishment Act of 1801, which greatly reduced the United States Army and Navy, Decatur was discharged from the Navy on October 22, 1801.