It serves the MBTA Orange Line and is located below grade at Boylston Street in the Jamaica Plain neighborhood.

[7][8] The final wooden bridges on the railroad's mainline were eliminated in the early 1880s when Stony Brook was rerouted to the east side of the tracks.

[1] Although the five NYNH&H stations in Roxbury and Jamaica Plain continued to operate for over three decades following the southward extension of the Washington Street Elevated, they were ultimately unable to compete with the Elevated, and all, including Boylston Street, were closed on September 29, 1940 due to a lack of passengers.

[13]) The Washington Street Elevated was permanently closed on April 30, 1987, and the new southern half of the Orange Line, including Stony Brook, opened on May 4.

[1] The entire Orange Line, including Stony Brook station, was closed from August 19 to September 18, 2022, during maintenance work.