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.
When Flowerfield station (west) ceased operations in 1958 and Setauket station (east) shut down in 1980, Stony Brook station became the preceding terminal on the Port Jefferson Route.