Brookhaven was a station stop along the Montauk Branch of the Long Island Rail Road located at Bridge Street and Old Stump Road (former Suffolk County Route 21).

In May 1958, the Long Island Rail Road (LIRR) applied to the New York State Public Service Commission for permission to close Brookhaven, East Moriches, and Eastport.

The LIRR sought to close the three stations due to very low ridership.

A ridership survey conducted in September 1957 found no passengers at Brookhaven.

[2] The former freight house has been moved to various private locations since 1958, and modified by each owner.