This station first appeared on timetables of the Central Railroad Extension Company of Long Island (a CRRLI subsidiary) in May 1873, though service may have been delayed a month or two.

The station depot itself was not built until either August or September 1873, and was located on the east side of Main Street just south of W. C. Dupignac's Hotel.

The station was reopened by the Long Island Railroad in June 1936 with a sheltered platform for a stop named "South Farmingdale.

"[3][4] In January 1945, local residents petitioned the Public Service Commission to have some Montauk express trains stop at South Farmingdale.

The move was opposed by residents of Bay Shore and Islip who thought that it would make the trains too crowded.