Farmingdale station was originally opened on October 15, 1841,[3] when the Long Island Rail Road first went through the village.

[4] The Main Line was electrified from Hicksville to Ronkonkoma in 1987, and the Farmingdale station began serving electric trains in June 1987; the electrified line east of the station, meanwhile, was not officially in service until December 1987.

[4] On November 13, 1991, the station house was added to the National Register of Historic Places.

[5] In 1996, federal funding from the Intermodal Surface Transportation Efficiency Act was obtained to restore the station building.

[8] In 2009, approximately 29 percent of all attendees arrived via the Long Island Rail Road.