The Junction City and Fort Kearney Railroad, a subsidiary of the Kansas Pacific Railway, was incorporated in Kansas in June 29, 1871. Construction started on its line at the Kansas Pacific mainline at Junction City and advancing north to Clay Center, completed on March 12, 1873. There, the JC&FtK connected with the Leavenworth, Kansas & Western Railroad.
In 1878, the line was extended further north to Concordia and a connection with the Missouri Pacific and the Chicago, Burlington and Quincy Railroads. Following on May 29, 1899, the JC&FtK, along with the Kansas Pacific, was merged into Union Pacific Railroad, who continued using the line under the name of the Junction City Branch (or also the Fort Kearney Branch). For most of its length between Clay Center and Concordia, the JC&FtK ran parallel and adjacent to the Chicago, Rock Island and Pacific Railroad.
In 1884, the JC&FtK was extended once again, this time between Lawrenceburg, on the line east of Concordia, northwards to Belleville. This was known as the Belleville Branch under the Union Pacific.
The Clay Center-Concordia segment was formally abandoned in 1933 by the Union Pacific when they decided to utilize trackage rights across the LK&W to Miltonvale and then over the Athcison, Topeka and Santa Fe Railroad north to Concordia (as submitted in the ICC filing below); this abandonment filing also included the branch line to Belleville. The remainder of the line between Junction City and Clay Center was abandoned by Union Pacific in 1964 when Milford Lake was dammed over the right-of-way just north of Junction City.