When the Flowerfield station (to the west) closed in 1958 and the Setauket station (to the east) closed in 1980, Stony Brook station became the penultimate station on the Port Jefferson Branch.
Following the closure of Flowerfield station in 1958 and Setauket station in 1980, Stony Brook station took its place as the last stop before Port Jefferson on the branch line.