In 1879 construction of tracks connecting the Union Pacific's main line at Grand Island with the St. Joseph and Western Railroad at Hastings provided a key link in a railroad empire controlled by New York financier, Jay Gould. The link freed the Union Pacific from the competition of connecting lines at its eastern terminus in Omaha by providing a route bypassing Iowa.
Like other railroads built throughout Nebraska in the 1880s, the St. Joe contributed to local settlement and development. In 1879 local pioneer William J. Burger platted the town of Doniphan midway between Grand Island and Hastings. The village and township were named after Col. John Doniphan of St. Joseph, Missouri, an attorney for the railroad.
After completion of the Grand Island line, the railroad was reorganized as the St. Joseph and Grand Island Railroad and for most of its history was part of the Union Pacific system. Construction of a Hastings to Gibbon cutoff in 1914 provided a shorter route to the Union Pacific main line, and use of the line through Doniphan gradually declined. It was abandoned in 1989.