Interest in establishing a railroad line that would later become known as the Central Branch Railroad (CBRR) started in Atchison, Kansas. In 1865, local prominent businessmen determined that Atchison was an ideal crossing point between Chicago to the southeast and St. Louis to the northwest. Believing that Atchsion would surpass the cities of St. Joseph and Kansas City as a railroad destination point, the businessman formed the Atchison and Pikes Peak Railroad.

In the spring of 1866 construction began on a line from Atchison to Netawaka, Kansas. This new line was named the Central Branch Railroad upon its completion in 1866. Track was laid further west to Waterville in the following year completing the first 100 miles. Plans were to continue the railroad line westward to Colorado, however, they were halted in 1869 when the Union Pacific Railroad bridged the Missouri River in Kansas City and took control of CBRR. In 1899, the railroad was named the Missouri Pacific Railroad, and again in 1908, but finally rested on the name used today in 1909.

Still under the control of the Union Pacific Railroad, the largest portion of CBRR, from Atchison to Frankfort, Kansas, was doomed to abandonment in 1999. In 2001, paperwork for the the last remaining portion of the CBRR line in Marshall County was filed for abandonment. The Marshall County Railroad Historical Society was formed to protect this significant historical aspect of the county.