The line crossed the Myrtle Avenue Elevated at grade two blocks south of its merge with the Brooklyn Elevated. On its second day of operation, November 6, a Hudson Avenue train crashed into a Myrtle Avenue train. Service was suspended immediately, and did not resume until June 22, 1889, when an extension south to Third Street was completed, and a new connection into Myrtle Avenue opened, taking trains between Third Street and Sands Street at the end of the Myrtle Avenue Elevated, and replacing the four track crossings with one. The unused two blocks north of Myrtle Avenue were placed back in service on December 9, 1889, when Myrtle Avenue trains began to use it to reach Fulton Ferry via the old Brooklyn Elevated.
An extension south to 25th Street at Greenwood Cemetery was opened at 4 p.m. on August 15, 1889. At this new terminal, elevated passengers could transfer to the north end of the Brooklyn, Bath and West End Railroad for Coney Island. A further extension to 36th Street, at a new Union Depot serving the West End Line and Prospect Park and Coney Island Railroad (Culver Line) to Coney Island, opened on May 29, 1890.
The Seaside and Brooklyn Bridge Elevated Railroad was organized on March 18, 1890 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, and to build in High Street at the Brooklyn Bridge (this became part of the Sands Street station loop). The extension of the Fifth Avenue Elevated, along Fifth Avenue, 38th Street, and Third Avenue, opened to 65th Street on October 1, 1893.
|Fulton Street||Hudson Avenue and Fulton Street||July 27, 1889||connection to Fulton Street Elevated trains and Fulton Street Line, DeKalb Avenue Line, and Flatbush Avenue Line streetcars|
|Atlantic Avenue||Flatbush Avenue and Atlantic Avenue||November 5, 1888||connection to Long Island Rail Road Atlantic Division trains at Flatbush Avenue terminal and St. Johns Place Line, Flatbush Avenue Line, Third Avenue Line, and Seventh Avenue Line streetcars|
|St. Marks Avenue||Fifth Avenue and St. Marks Place||June 22, 1889||connection to Bergen Street Line streetcars|
|Union Street||Fifth Avenue and Union Street||June 22, 1889||connection to Union Street Line streetcars|
|3rd Street||Fifth Avenue and Third Street||June 22, 1889|
|9th Street||Fifth Avenue and Ninth Street||August 15, 1889||connection to Smith and Ninth Streets Line and Hamilton Avenue Line streetcars|
|16th Street||Fifth Avenue and 16th Street||August 15, 1889||connection to 15th Street Line streetcars|
|20th Street||Fifth Avenue and 20th Street||August 15, 1889|
|25th Street||Fifth Avenue and 25th Street||August 15, 1889|
|36th Street||Fifth Avenue and 36th Street||May 29, 1890||connection to West End Line trains|
|40th Street||Third Avenue and 40th Street||October 1, 1893||connection to Church Avenue Line, 39th Street and Coney Island Line, 39th Street and Manhattan Beach Line, and 39th Street and Ulmer Park Line streetcars|
|46th Street||Third Avenue and 46th Street||October 1, 1893|
|52nd Street||Third Avenue and 52nd Street||October 1, 1893|
|58th Street||Third Avenue and 58th Street||October 1, 1893|
|65th Street||Third Avenue and 65th Street||October 1, 1893||connection to Sea Beach Line, Bay Ridge Suburban Line, Bay Ridge Line, Third Avenue Line, and 86th Street Suburban Line streetcars|