The Canarsie Railroad was chartered on May 8, 1906 as a BRT subsidiary (leased to the Brooklyn Union Elevated Railroad) and acquired the line on May 31, 1906. The line was partly elevated, and electrified with third rail on the elevated part and trolley wire on the rest, south of New Lots Avenue. The Long Island Rail Road, which had used the line north of New Lots to access their Bay Ridge Branch, built a new line just to the west. The East New York terminus was extended several blocks along a section of line formerly used for "East New York Loop" service to the Fulton Street Elevated and the Broadway Elevated (now the BMT Jamaica Line), at a point known as Manhattan Junction (now Broadway Junction).
Service, first run on July 28, 1906, ran from Canarsie Landing to the Broadway Ferry at the foot of Broadway in Williamsburg, at the East River. This route still exists as the BMT Jamaica Line, except for the last piece to the East River, where the Jamaica Line runs over the Williamsburg Bridge. The route was later extended over the bridge and along the BMT Nassau Street Line to Canal Street and then Chambers Street.