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Rail service in Beacon can be traced as far back as December 6, 1849, with the Hudson River Railroad. The station was originally named "Fishkill Landing," and like many others on the Hudson Line, it is also right on the Hudson River. On September 4, 1866, the Dutchess and Columbia Railroad was established with the hope of running from the south side of Fishkill Creek northeast and north to meet the New York and Harlem Railroad at Craryville, New York. This junction and the station were built south of Fishkill Landing, and would be known forever as Dutchess Junction. The first station at Dutchess Junction, which was shared by the NYC&HR and D&C was burned down in April 1876, and rebuilt. The railroad along the river was acquired by the New York Central and Hudson River Railroad in November 1869. By 1877, the D&C was taken over by the Newburgh, Dutchess and Connecticut Railroad. In 1881 the New York and New England Railroad built a ferry port near Fishkill Landing station, and added a connecting spur along the north side of the Fishkill Creek (now known as the Beacon Secondary) leading to what became Wickopee Junction, and turned it over to the ND&C.