In 1806, Johnson was elected as a Democratic-Republican to the United States House of Representatives, serving as the first native Kentuckian to be elected to Congress. In the three-way election, he defeated Congressman Sandford and James Moore. At the time of his election in August 1806, he did not meet the U.S. Constitution's for service in the House (25), but by the time the congressional term began the following March, he had turned 25. He was re-elected and served six consecutive terms. During the first three terms from 1807 to 1813, he represented Kentucky's Fourth District.