The son of a distinguished naval officer, Jonathan Faulknor continued the family tradition and forged a career in the navy. He was made an officer prior to the Seven Years' War and commanded his first ships before it ended. His service was punctuated by periods without command of a ship, and times as captain of guardships. Nevertheless he was able to impress his superiors with his services, including his cool handling of a crisis when his ship ran aground off Cork. He was back in command of ships during the American War of Independence, and was flag captain to Admiral Keppel at the battle of Ushant in 1778. He captained several other ships during the war, relieving Gibraltar in 1782 with Howe and seeing action at the Battle of Cape Spartel.