The station opened in 1905 as an extension of the Interborough Rapid Transit (IRT)'s original subway line to South Ferry.

The station retains its original head house in Battery Park, which is listed on the National Register of Historic Places and a New York City designated landmark.

[6]: 21  However, development of what would become the city's first subway line did not start until 1894, when the New York State Legislature passed the Rapid Transit Act.

[12][13] The New York Times wrote that the installation of the switches between the loop and the main line presented "an engineering problem of great difficulty".

[12] Work on the section of line from Ann Street (just south of City Hall) to Bowling Green had not started by September 1903, and McDonald blamed Parsons for the delays.

[14][15] The dispute was quickly resolved, as neither man had realized that the other did not want the project to disturb daytime traffic along Broadway; work started shortly thereafter.

[19][20] After the Joralemon Street Tunnel opened in 1908,[22][23] ticket sales increased at Bowling Green and the IRT's other subway stations in Lower Manhattan.

[26] Three months after the Joralemon Street Tunnel opened, construction began on the third track and the western island platform at Bowling Green.

[27] Even after the IRT Broadway–Seventh Avenue Line local service (1 train) began to South Ferry in 1918, the shuttle remained in operation until it was discontinued in 1977 due to budget cuts.

[28] To address overcrowding, in 1909, the New York Public Service Commission proposed lengthening the platforms at stations along the original IRT subway.

[29]: 168  As part of a modification to the IRT's construction contracts made on January 18, 1910, the company was to lengthen station platforms to accommodate ten-car express and six-car local trains.

[35][36] On September 8, 1952, the New York City Board of Transportation made the entrance kiosk at Battery Place and State Street entrance-only instead of exit-only in order to relieve congestion at the station during the evening rush hour.

[37] The New York City Transit Authority (NYCTA) announced plans in 1956 to add fluorescent lights above the edges of the station's platforms.

[39] NYCTA architect Harold Sandifer prepared plans in the late 1950s for a modern-style station house within Bowling Green Park, which would contain a brick-and-aluminum facade, along with planters containing dwarf Japanese yew trees.

[41][42] The NYCTA approved a proposal in September 1960 to install an experimental token-vending machine, which would dispense advertisements along with tokens, at the Bowling Green station.

[46] As early as the mid-1960s, local civic group Downtown-Local Manhattan Association had raised concerns that the Bowling Green station was severely overcrowded during rush hours.

[55] Stairs and a new mezzanine were built below track level, and a new exit with modern escalators was installed just south of Bowling Green.

[57][58] The new mezzanine, excavated under Bowling Green Park using a cut-and-cover method, was connected to the platform and street levels with ten new escalators.

[51][52] These capacity improvements were made to accommodate increased ridership resulting from the construction of additional office buildings in Lower Manhattan, including the World Trade Center.

[76] Following the September 11 attacks in 2001, members of the public expressed concerns that the station could be difficult to evacuate in emergencies due to its convoluted layout.

[82][83] The MTA added a hearing induction loop for passengers on the northbound platform, the first such installation in the subway system, during a pilot program in 2020.

[84][85] The MTA announced in December 2021 that it would install wide-aisle fare gates for disabled passengers at five subway stations, including Bowling Green, by mid-2022.

[94] The station is between Wall Street to the north and Borough Hall in Brooklyn to the south; it is the southern terminus for the 5 train during weekends and mid-weekday evenings.

Custom House, just around the corner from two entrances to the Whitehall Street–South Ferry station on the BMT Broadway Line (which are set into the building's eastern elevation).

[92] This subway entrance was designed by Heins & LaFarge and built in 1905 on the west side of State Street, across from the Alexander Hamilton U.S.

[4] The facade is made of yellow brick, with limestone banding and triglyphs at its tops, a base of granite, and a gable roof.

Inside, the control house has turnstiles at street level and a single stair down to the extreme southern end of the island platform.

Since 2018, the exhibition has been "Daily Voyage", featuring pictures taken by Glen DiCrocco of regular commuters on the Staten Island Ferry.

[122] There are numerous skyscrapers and other structures immediately surrounding the Bowling Green station (listed clockwise): Another park, the Battery, is located right outside the southern entrance.