Stony Brook is a station on the Port Jefferson Branch of the Long Island Rail Road.

[5][6] Despite the impact of the arrival of Stony Brook University in 1957, the station has remained a small one-story depot.

Parking has always been limited, but efforts to increase capacity at the station have been attempted both by SUNY and NYSDOT.

In 1989, the station underwent a renovation project, including 12-car-long high-level platforms, a pedestrian overpass, and straightening of the tracks, as well as a new parking lot on the Stony Brook University campus.

[7][8] Beginning in April 2010, the Metropolitan Transportation Authority planned a renovation project that was intended to last until January 2011.