The Junction City and Fort Kearney Railroad, a subsidiary of the Kansas Pacific Railroad, was incorporated in Kansas on June 29, 1871. Construction started on its line at the Kansas Pacific mainline at Junction City and advanced north to Clay Center. It was completed on March 12, 1873. There, the Junction City and Fort Kearney Railroad connected with the Leavenworth, Kansas & Western Railroad.
In 1878, the line was extended north to Concordia to connect with the Missouri Pacific Railroad and the Chicago, Burlington, and Quincy Railroads.
In 1884, the Junction City and Fort Kearney Railroad was extended again, this time between Lawrenceburg, on the line east of Concordia, and northwards to Belleville. This was known as the Belleville Branch under the Union Pacific.
After 28 years of operation, the Junction City and Fort Kearney Railroad, along with the Kansas Pacific Railroad, was merged into the Union Pacific Railroad on May 29, 1899, which continued using the line under the name of the Junction City Branch or the Fort Kearney Branch, for most of its length between Clay Center and Concordia, the Junction City and Fort Kearney Railroad ran parallel and adjacent to the Chicago, Rock Island & Pacific Railroad.
The Clay Center-Concordia segment was formally abandoned in 1933 by the Union Pacific Railroad when they decided to utilize trackage rights across the Leavenworth, Kansas & Western Railroad to Miltonvale and then over the Atchison, Topeka & Santa Fe Railroad north to Concordia. This abandonment filing also included the branch line to Belleville in 1934. The remainder of the line between Junction City and Clay Center was abandoned by the Union Pacific Railroad in 1964 when the Republican River was dammed over the right-of-way just north of Junction City to create Milford Lake.