Stony Brook is a historic station on the Port Jefferson Branch of the Long Island Rail Road. It is located in Stony Brook on the southeast side of New York State Route 25A, across the street from the intersection of Route 25A with Cedar Street. On the opposite side of the tracks is the State University of New York at Stony Brook. There is also a gated at-grade pedestrian crossing between the station and a parking lot at the University. The station is one of only two such stations on the Long Island Rail Road to exclusively feature such crossings, the other being Westwood. This train station is located in the Three Village Central School District.