Johnson was elected to the House of Representatives in 1806 in the early Federal period. He became allied with fellow Kentuckian Henry Clay as a member of the War Hawks faction that favored war with Britain in 1812. At the outset of the War of 1812, Johnson was commissioned a colonel in the Kentucky Militia and commanded a regiment of mounted volunteers from 1812 to 1813. He and his brother James served under William Henry Harrison in Upper Canada. Johnson led troops in the Battle of the Thames. Many reported that he personally killed the Shawnee chief Tecumseh, a claim that he later used to his political advantage.