The Rock Island Railroad came into Manhattan in 1887, completing the city's railroad system. The road ran south of the Manhattan, Alma, and Burlingame Railroad line from Wabaunsee to Manhattan and crossed the town on El Paso Street, a block north of the Union Pacific tracks. The depot was stationed betweeen 4th and 5th streets. The company name was the Chicago, Kansas & Nebraska Railway, but later changed to the Chicago, Rock Island & Pacific in 1889. A new railroad bridge across the Kansas River was built on the east side of Manhattan and a sixty-foot deep cut was made in the south end of the hill where Wildcat Creek joined the Kansas River. From there the railroad followed Wildcat Creek northwest through Keats and Riley,` then on to Clay Center, connecting to the main line at Belleville, Kansas. The Manhattan to Alma section of the Manhattan, Alma, & Burlingame Railroad was abandoned in 1898.
Manhattan worked to establish additional railroad connection. The Manhattan and Northwestern Railroad up the Blue Valley was started in 1872 and reasched Cleburne and Randolph by 1885. After 1881, the Blue Valley line connected to the Leavenworth, Kansas, and Western (LK&W) Railroad which ran from Leavenworth to Miltonvale through northern Riley County. The Manhattan, Alma, and Burlingame Railroad ran between 1881 and 1903 while the Chicago, Rock Island, and Pacific Railroad line operated from 1887 to 1980.