[2] As these locomotives could not be used for freight operations, the line was electrified in 1899; however, the LIRR occasionally ran steam-powered special trains to the Brooklyn Jockey Club Racetrack at Kings Highway and Ocean Parkway.

It carried mail for the U.S. Post Office Department, as well as lumber, cement, sand, stone, ashes, pipe, marble for headstones, and granite for curbstones.

The South Brooklyn Railway was a separate subsidiary company that carried both passengers and freight, to avoid the BRT from being operated under Interstate Commerce Commission regulations.

[2] In 1909, the South Brooklyn Railway was granted a request by the Public Services Commission to discontinue the use of the Third Avenue freight yard and station, on the Prospect Park and Coney Island Railroad's property.

[2] The South Brooklyn Railway, along with the other non-rapid transit properties of the BMT, was transferred to the New York City Board of Transportation on June 1, 1940.

[6] Passenger service on McDonald Avenue ended on October 31, 1958, and thereafter the South Brooklyn Railway started using the surface trackage solely for freight.

[2] The switches at Kensington Junction were locked so that the branch was completely separated up to the Ninth Avenue & 20th Street Depot, which thereby became an unneeded facility because passenger streetcar operation had ended.

[2] The South Brooklyn Railway provides one of only two track connections between the New York City Subway and the rest of the American rail network.

During the 1988 and 1999 reconstruction of the subway tracks on the Williamsburg Bridge, this connection allowed trains from the J/Z, L and M services, which were otherwise isolated during that period, to travel to Coney Island Yard for major work.

A new ramp was installed at the 38th Street Yard at Fourth Avenue to allow receipt of new R156 locomotives and other subway rolling stock that were delivered on flat cars.