Trains began operating between Fulton Ferry (the terminal of the Brooklyn elevated) and Flatbush Avenue on November 5, 1888.

[10] The Long Island Rail Road (LIRR) had service on the elevated line from Brooklyn Bridge, through Atlantic and Flatbush Avenues to the 36th Street Union Depot, connecting with the Manhattan Beach Line starting in 1895.

[citation needed] The Seaside and Brooklyn Bridge Elevated Railroad was organized on March 18, 1890[11] to extend the Fifth Avenue Elevated south to Fort Hamilton, to extend the Lexington Avenue Elevated from Van Siclen Avenue east to the city line,[12] and to build in High Street at the Brooklyn Bridge (this became part of the Sands Street station loop).

[16][17] At midnight on June 1, 1940, service on the Fifth Avenue Elevated ended as required by the unification of the city's three subway companies.

In total, three miles of the elevated were scrapped, with the work being done by the Harris Structural Steel Company.