The project, first announced in 2002, was intended to improve access to and connections among the New York City Subway services stopping at the Fulton Street station.

Funding for the construction project, which began in 2005, dried up for several years, with no final approved plan and no schedule for completion.

Ten escalators and fifteen elevators were installed, as well as two ADA accessible public restrooms on the concourse and the street levels.

According to the MTA's Final Environmental Impact Statement, the Dey Street Passageway is intended to provide a seamless connection from the Fulton Center to the WTC Transportation Hub and Brookfield Place (formerly the World Financial Center) without the need to cross Church Street and Broadway, both of which are busy traffic arteries in Lower Manhattan.

[19][20] As part of this initiative, money was also to be allocated to study the feasibility of commuter rail service to Lower Manhattan.

[22] As part of the rebuilding process, the Port Authority considered putting the PATH terminal at Broadway and Fulton Street.

[23] The Port Authority ultimately decided to put the PATH terminal near Greenwich Street, two blocks west.

[10]: 14–15 In February 2003, New York Governor George Pataki announced a $5 billion plan for rebuilt transit infrastructure at South Ferry, Fulton Street, and the World Trade Center.

[27] By April 2003, the MTA had released preliminary plans for a $750 million transit hub at Fulton Street, connecting six subway stations.

[33][34] That year, a group of architecture firms, including Nicholas Grimshaw & Partners and Lee Harris Pomeroy Associates, were hired to design the Fulton Street Transit Center.

[36] A block to the north, the MTA began the process of evicting and relocating 148 store owners near the site of the transit center's main building.

[42] In November 2006, the MTA announced the creation of a free transfer between the Cortlandt–Church Streets and World Trade Center stations, which would cost $15 million more.

[12][53][54] In January 2009, the MTA received $497 million in additional stimulus money, bringing the total cost of the Fulton Street Transit Center to $1.4 billion.

The 115-year-old Corbin Building, at the corner of Broadway and John Street, will be restored and incorporated into the transit center entrance design.

[57] With funding secured in 2009, MTA Capital Construction released a plan to open various stages of the Fulton Center project.

[10]: 10  The renovation started after the entrances at Maiden Lane (northbound) and Cortlandt Street (southbound) were opened to ameliorate passenger flow during subsequent station rehabilitation.

This was completed in conjunction with the gradual opening of a transfer mezzanine over the IND Eighth Avenue Line platform, serving the A and ​C trains.

[69] Related construction work saw the temporary closure of the entrances at Fulton Street, on the northwest (by St. Paul's Chapel) and southwest corners throughout much of 2011.

[8] Originally, a network of passageways and ramps loosely connected the various lines with each other, causing congestion during peak hours.

In January 2010, reconstruction of the transfer mezzanine over the Fulton Street IND platform resulted in traffic flow changes.

[10] The stacked-staggered configuration of the BMT Nassau Street Line platforms splits the IND mezzanine levels into halves.

In June 2012, an underpass under the Lexington Avenue Line platforms, traveling approximately under Fulton Street, re-opened and was connected to the Western Mezzanine.

With the opening of the new passageway, the older underpass connecting to southbound Lexington Avenue Line platform was simultaneously closed.

[14] It serves as an entrance for the southbound Lexington Avenue Line trains, and as the main access point for the long-anticipated Dey Street Passageway.

[78][79][80] Sky Reflector-Net, which was commissioned as part of MTA Arts & Design program, was installed in 2014 in the Fulton Center transit hub.

Located at the center of the oculus, the Sky Reflector-Net uses hundreds of aluminum mirrors to provide natural sunlight from a 53 ft (16 m) skylight to an underground area as much as four stories deep.

[90] In July 2012, the MTA made a motion to seek proposals from various companies for a master lease for 65,000 square feet of retail and commercial space.

Originally slated to be demolished, the building was instead restored as a part of the Fulton Center project and incorporated to the overall transit complex.

[99] A separate transfer to the 1 train at WTC Cortlandt, outside the fare controls of either the Cortlandt–Church/World Trade Center or Fulton Street stations, was opened on September 8, 2018.

[16] In February 2024, media sources reported that Westfield was trying to terminate its lease at the Fulton Center ten years early.