The complex is located in the vicinity of MetroTech Center (near Jay and Willoughby Streets) in Downtown Brooklyn.

Both stations also contain "money train" platforms, which were formerly used to deliver MTA token revenue to neighboring 370 Jay Street.

[7] In 1916, local business owners proposed an additional station at Lawrence and Willoughby Streets.

Only one-ninth of the labor estimated to be required to allow the construction of the station to be completed along with the rest of the line was available.

The scope of work included excavation from the street to provide an entrance, the construction of an island platform between the two cast iron-lined tunnels covered by a steel and concrete roof, and the construction of a passageway, mezzanine and entrances.

In response to increased ridership at the station from traffic MetroTech generated, new directional signs were installed, a wall that blocked the view of the token booth clerk was removed to improve security, a part-time token booth was added, and lighting was upgraded.

[13] New York City mayor John Francis Hylan's original plans for the Independent Subway System (IND), proposed in 1922, included building over 100 miles (160 km) of new lines and taking over nearly 100 miles (160 km) of existing lines, which would compete with the IRT and BMT.

[14][15] On December 9, 1924, the New York City Board of Transportation (BOT) gave preliminary approval for the construction of the IND Eighth Avenue Line.

[19] The Jay Street–Borough Hall station was part of a three-stop extension of the IND Eighth Avenue Line from Chambers Street in Lower Manhattan.

[30] In 1957, the city conducted another experiment, this time placing an automatic token dispenser in the station.

[41] The $164.5 million project also brought the stations into compliance with the Americans with Disabilities Act of 1990[2][42] and cosmetically improved the upper mezzanine.

[2] In 2016, a new entrance to the BMT portion of the station was built as part of the AVA DoBro residential high-rise building.

[53] It was installed as part of the MTA Arts for Transit program during the station complex's renovation.

The one at the north end has a weekday-only turnstile bank and token booth, full height turnstiles, and a wide staircase to MetroTech Center and another stair and four escalators to the former New York City Transit Headquarters,[55] a mostly vacant 13-story building at 370 Jay Street.

[50][54] These escalators were installed as part of a 1952 improvement, as were the squarish "Subway" entrance lamps that are found only in a few other places in the system.

[57] The building itself has a memorial to New York City Transit workers who died in World War II.

[55] The entrance/exit at the south end has only full height turnstiles and two staircases leading to either side of Jay and Fulton Streets.

This fare control area was the first in the system to have its service gate converted to an emergency exit.

[51][54] The AVA DoBro building contains stairs and an elevator, which connect to the eastern, full-height turnstile entrance.

[60] Before renovation, the trim line on the platform walls was two-tone cobalt blue with "JAY" tiled in white lettering on a black background underneath.

[51] A narrow mezzanine above the platform connects the station's two easternmost fare control areas.

[51] The platform formerly had a narrow up-only escalator that bypassed the Lawrence and Willoughby Streets fare control, and led to a small landing with two high exit-only gates.

[51] Formerly, "money trains" collected the tokens that were used to pay fares at each of the subway stations and deposited them into a special door that led to a money-counting room under 370 Jay Street.

[65] The platforms were placed next to 370 Jay Street because it was a convenient location near where all three subway companies had tunnels.

[68] A third platform is also in the IRT Eastern Parkway Line tunnel that passes through this area for the same purpose.