He was appointed a midshipman at age 21 on 28 April 1800. His brother Robert Livingston also served in the U.S. Navy as a surgeon on the frigate during the War of 1812. His other brother, Herman, was purser on the USS Wasp and the USS Peacock. Jonathon Thorn served in the Navy during the Tripolitan War, and volunteered to take part in the hazardous expedition to destroy the captured frigate "Philadelphia", which was moored beneath the guns of the defended Tripoli harbor. On 16 February 1804, Lieutenant Stephen Decatur led a party of these volunteers in the ketch "Intrepid" into Tripoli and burned the American ship so it could not be used by the enemy.