Warner then moved his practice to Kansas City, where he served as city attorney in 1867, circuit attorney in 1868, and as the mayor of Kansas City, Missouri in 1871. He was elected as a Republican to the 49th and 50th Congresses, serving from March 4, 1885 to March 3, 1889, but he was not a candidate for renomination in 1888.
Warner unsuccessfully ran as the Republican candidate for Missouri Governor in 1892, but served as the United States district attorney for the western district of Missouri in 1882-1884, 1898, and 1902–1905. In 1882, he was one of the original incorporators of the Kansas City Club.[3]
Warner resumed the practice of law and was appointed as a civilian member of the Board of Ordnance and Fortifications and a member of the Board of Managers of the National Home for Disabled Volunteer Soldiers. His widow, Sophia, received a pension until her death in 1923.