The station opened as Manhattan Junction as part of the BMT Lexington Avenue Line in 1885. In 1900, an elevated connection was made with the Fulton Street Elevated, resulting in a change in service patterns. Lexington Avenue and Fulton Street trains were through-routing, going around the East New York Loop, with service to Cypress Hills requiring a transfer. The station started to be used by service to Canarsie in 1906. In 1919, the Manhattan Junction station was replaced by the current station which was then known as Eastern Parkway. The modern-day Canarsie Line platforms, known as Broadway Junction, opened in 1928 when that line was connected to the 14th Street–Eastern District Line. The Independent Subway System's Fulton Street Line was extended to Broadway–East New York in 1946, and the three stations were combined as one station complex on July 1, 1948. The names of the stations in the complex were conformed to Broadway Junction in 2003.