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.