History - A subsidiary of the Atchison, Topeka and Sante Fe Railroad, the Kansas City, Emporia, and Southern Railway Company, developed plans to build a railroad from Emporia through Madison and on to Howard, Kansas. Thus it was known as the Howard Branch.
Before the rails reached old Madison on the river, the Depot was built in its current spot in modern-day Madison. Since the railroad had bypassed them, and believing their location was really ill-suited for a town due to the tight confine of the river bend and the low-lying area that was forever damp, the town leaders decided to move the town. The depot seemed like a likely place. The land was available. The move was made and that's how Madison came to be located where it is.
The railroad was the lifeline of the community. Almost everything necessary for life in Madison, which could not be raised or manufactured locally, was shipped by rail. Likewise, those commodities which brought income to area inhabitants - livestock, hay and grain, and later, oil - were sent to markets across the country, via the train. Passenger service was also available.
Madison would actually be served by three railroads: The Howard Branch as noted; the Interstate Road (Missouri Pacific - 1886); and the River Road (another subsidiary of the Sante Fe known as the Chicago, Kansas & Western) which went through Virgil on its way to Chanute. One by one, these would drop by the wayside, with the last train running through Madison in 1975.

The depot was placed on the National Register of Historic places in 1991. It has been fully restored and now serves as a museum.

Thank you to Bob Robison for the history on the Sante Fe Depot.

                                      
                                                     The Santa Fe Depot in 1964. Photo from kansasmemory.org