Nathaniel Fanning (31 May 1755 – 30 September 1805) was an officer in the United States Navy who fought onboard Bonhomme Richard

Born in Stonington, Connecticut, Fanning was commissioned midshipman in France by John Paul Jones when he was manning Bonhomme Richard. In the victory over Serapis 23 September 1779, Fanning served as captain of the main top. Most of his original group of men were killed, but he took a fresh party aloft and with them cleared Serapis' tops. When their yards locked the ships together, he led his men across to the British ship, where with hand grenades and other missiles, they drove the British seamen from their stations. In recommending that Fanning be promoted, Jones said of him ". . . he was one cause among the prominent in obtaining the victory".

Lieutenant Fanning died of yellow fever 30 September 1805 while commanding Gunboat Number 1.

Two ships in the United States Navy have been named USS Fanning for him.