In September 1861, Governor Robinson appointed him judge of the Second judicial district. Later he was elected to the position twice without opposition, eventually resigning to resume his law practice. From 1861 to 1864 he was a member of the editorial staff of the Atchison Weekly Champion. In 1868 he was a Republican presidential elector and was elected as messenger to carry the vote of the state to Washington. In May, 1869, President Grant appointed him United States district attorney for Kansas. He was elected to the Kansas House of Representatives in 1872, and to the Kansas Senate in 1876, but resigned on January 1, 1877, to accept the appointment of chief justice offered by Governor Osborn. Later that year, Horton was elected to that office to fill the unexpired term. He was reelected in 1878, 1884 and 1890. In 1885 his name was presented to the joint session of the legislature for United States senator, and on the first ballot the vote stood 86 for John J. Ingalls and 83 for Judge Horton.
