Following the cessation of hostilities with France, Midshipman Warrington remained in the Navy. His ship spent most of 1801 in ordinary at Norfolk. The following year, Warrington was transferred to the frigate President for service in the Mediterranean against the Barbary pirates. Over the next five years, he remained with the Mediterranean Squadron, serving successively in President, Vixen, and Enterprise. Promoted to lieutenant in 1805, he returned home in 1807 to assume command of a gunboat at Norfolk, Virginia. In 1809, Lt. Warrington voyaged to Europe in Siren as a dispatch courier. He next served a tour of duty in Essex.
When the war with England began in June of 1812, Warrington was in Congress serving as the frigate’s first lieutenant while she patrolled the North Atlantic. During his tour of duty in that warship, she made two successful war cruises, capturing nine prizes off the east coast of the United States during the first and four off the Atlantic seaboard of South America during the second.
Promoted to master commandant in July 1813, he took command of the sloop-of-war Peacock later in the year. On 12 March 1814, he put to sea with his new command bound for the naval station at St. Marys, Georgia. After delivering supplies to that installation, he encountered the British brig Epervier off Cape Canaveral, Florida. Peacock emerged victorious from a brisk 45-minute exchange with that opponent, inflicting 10 times her own losses on the enemy. For his role in the victory, Warrington received the thanks of Congress in the form of the Congressional Gold Medal, and of the state of Virginia in the form of a gold-hilted sword.
Warrington took his prize into Savannah, Georgia and then embarked upon his second cruise on 4 June. On that voyage—which took him to the Grand Banks, the Irish coast, the Shetland Islands, and the Faroe Islands —he took 14 prizes.
After returning via the West Indies to New York, Warrington took Peacock on her third and final war cruise. His sloop-of-war stood out of New York with Hornet and Tom Bowline on 23 January 1815, sailed around the Cape of Good Hope, and entered the Indian Ocean. Unaware that peace had been concluded in December 1814 at Ghent, Belgium, Warrington led his little force on another successful foray against British commerce. After taking three prizes in the Indian Ocean, he entered the East Indies in search of more game. On 30 June, he encountered the East India Company cruiser Nautilus in the Sunda Strait and attacked her. After a sharp action which cost the British ship 15 men including her first lieutenant, she surrendered to Warrington and his force. At this point, Warrington learned of the peace, and he therefore released the prize and started for home. Peacock arrived back in New York on 30 October 1815.
In 1816, he commanded Macedonian briefly for a voyage to Cartagena, Spain, to convey there Christopher Hughes, the representative of the United States at negotiations over the release of some Americans imprisoned by Spanish authorities. In 1819 and 1820, Capt. Warrington commanded Java, followed by Guerriere in 1820 and 1821. Each ship was assigned to the Mediterranean Squadron during his tenure as her commanding officer. Capt. Warrington returned home and received orders to duty at the Norfolk Navy Yard. In February 1825, he relieved Porter as commander of the West Indian Squadron during the latter stages of the piracy suppression campaign and thereafter bore the title, commodore.
In 1826, Warrington returned home and served ashore for the remainder of his career. After four years in Washington—1826 to 1830—as one of three commissioners on the Navy Board, a body charged with the administration of naval materiel, Warrington returned to Norfolk for a decade as commandant of the navy yard. In 1840, he was reassigned to Washington for another two years as commissioner on the Navy Board. After the 1842 reorganization of the Navy Department, Warrington became Chief of the Bureau of Yards and Docks.
On 28 February 1844, he took over temporarily the duties of the Secretary of the Navy after Secretary Thomas W. Gilmer died as a result of wounds received when the large cannon “Peacemaker” exploded during a firing demonstration on board Princeton at Washington. Near the end of March, Warrington relinquished those duties to the new secretary, John W. Mason, and resumed his former assignment. In 1846, he became Chief of the Bureau of Ordnance, which office he held until his death on 12 October 1851.