The station was constructed for the Interborough Rapid Transit Company (IRT) as the southern terminal of the city's first subway line, which was approved in 1900.

Construction of the segment of the line that includes the City Hall station started on September 12 of the same year.

The City Hall station, with its single track and curved side platform, was the showpiece of the original IRT subway.

The single platform and mezzanine feature Guastavino tile, skylights, colored glass tilework, and brass chandeliers.

[7]: 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.

They called for a subway line from New York City Hall in lower Manhattan to the Upper West Side, where two branches would lead north into the Bronx.

[7]: 161  The Rapid Transit Construction Company, organized by John B. McDonald and funded by August Belmont Jr., signed the initial Contract 1 with the Rapid Transit Commission in February 1900,[8] in which it would construct the subway and maintain a 50-year operating lease from the opening of the line.

[6]: 5 [10]: 14  When the plans for the IRT line were changed in 1898 to allow the express tracks to go to Brooklyn as part of the subway's Contract 2, the planned City Hall station was changed to a single-track local station, thereby avoiding a grade crossing with the express tracks.

[8][9]: 4  The tunnel was built using a cut and cover method, with steel beams supporting a concrete roof made of jack arches.

[24] Most of the excavation was covered over shortly afterward, although a small part remained open to facilitate work on the station.

[28] The contractors excavated the remainder of the loop after they were given temporary permission, in December 1902, to use the vaults underneath the post office.

[7]: 186 [31] On New Year's Day 1904, mayor George B. McClellan Jr. and a group of wealthy New Yorkers gathered at the City Hall station and traveled 6 mi (9.7 km) to 125th Street using handcars.

[5] Prior to the opening, more than 15,000 people were issued passes for the first series of rides from the City Hall station's platform.

[37] President A. E. Orr of the Rapid Transit Board requested that all New Yorkers join in the celebration by blowing whistles and ringing bells.

[9]: 4  After the Fulton Street station opened in January 1905,[40] the City Hall Loop was served by local trains to the West Side Branch at all times and by local trains to 145th Street on the East Side Branch (now Lenox Avenue Line) during the daytime.

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

[46]: 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.

[1]: 4 In its final years, the City Hall station was not open at night and on Sundays,[56][57] when trains continued to South Ferry.

[6][64] By the 1980s, Mayor Ed Koch suggested allowing a restaurant to open in the old station as part of a larger plan to renovate City Hall Park.

[71] Early the next year, MTA officials started refurbishing the station's corridors and offered up to $5 million for underground repairs to City Hall Park, which at the time was being renovated.

However, in late 1998, the administration of mayor Rudy Giuliani rejected the proposal, citing security risks in the area around City Hall after terrorist bombings in Nairobi and Dar es Salaam.

[77] The station consists of a single balloon loop track along a concave side platform, which has a length of 240 feet (73 m)[61] and could fit five subway cars.

According to NYTM officials, the station inspired the main characters' lair in the 1990 film Teenage Mutant Ninja Turtles.

[1]: 4  Additional lighting was supplied by twelve chandeliers hung from the center of the vaults, which contain floral motifs and nickel finishes.

[10]: 14 [1]: 4  On the platform walls are three blue-on-white faience plaques with letters reading city hall, flanked by a pair of triangles and surrounded by green and buff tiles.

[10]: 31  On the trackside wall, facing the platform, are three bronze plaques with the names of important figures involved in the original IRT's construction, including Parsons, McDonald, Belmont, Rapid Transit Subway Construction Company officials, engineering staff, mayors, commissioners, and city comptrollers.

[30] The mezzanine contains a vaulted ceiling with a quoin pattern, consisting of brown trim with white and green tiles.

[86] North of the City Hall station, the IRT Lexington Avenue Line carries four tracks.

When the loop was completed, Scientific American magazine wrote that "one of the more important tasks of constrictive engineering which the subway presented is solved".

[10]: 13  One critic said the station's original entrance and exit kiosks gave "a foreign appearance" to City Hall Park and compared the vaults to the interior of a mosque.