Johnson declined to run for reelection in 1852. He was appointed by the legislature to the United States Senate to fill the unexpired term of Senator Solon Borland. In 1855, he was elected by the legislature to the seat, serving the full term until 3 March 1861. After the outbreak of the American Civil War, he served as a delegate to the Provisional Government of the Confederate States in 1862. He served as a member of the Confederate Senate from 1862 to 1865.