Since the late 20th century, the Metropolitan Transportation Authority has started several projects to maintain and improve the New York City Subway. Some of these projects, such as subway line automation, proposed platform screen doors, the FASTRACK maintenance program, and infrastructural improvements proposed in 2015–2019 Capital Program, contribute toward improving the system's efficiency. Others, such as train-arrival "countdown clocks", "Help Point" station intercoms, "On the Go! Travel Station" passenger kiosks, wireless and cellular network connections in stations, MetroCard fare payment alternatives, and digital ads, are meant to benefit individual passengers. Yet others, including the various methods of subway construction, do not directly impact the passenger interface, but are used to make subway operations efficient.

In the mid-1990s, it started converting the BMT Canarsie Line to use communications-based train control, using a moving block signal system that allowed more trains to use the tracks and thus increasing passenger capacity. After the Canarsie Line tests were successful, the MTA expanded the automation program in the 2000s and 2010s to include other lines. This led to a 2017 proposal to install platform screen doors in one Canarsie Line station. Additionally, as part of another program called FASTRACK, the MTA started closing certain lines during weekday nights in 2012, with each of the lines closing overnight for a week in order to allow workers to clean these lines without being hindered by train movements. The program was expanded beyond Manhattan the next year after observing the increased efficiency of the FASTRACK program compared to previous service diversions. In 2015, the MTA announced a wide-ranging improvement program as part of the 2015–2019 Capital Program. Thirty stations would be extensively rebuilt under the Enhanced Station Initiative, and new R211 subway cars would be able to fit more passengers.

The MTA has also started some projects to improve passenger amenities. It added train arrival "countdown clocks" to most A Division (numbered route) stations and the BMT Canarsie Line () by late 2011, allowing passengers on these routes to see train arrival times using real-time data. A similar countdown-clock project for the B Division (lettered routes) and the IRT Flushing Line was deferred until 2016, when a new Bluetooth-based clock system was tested successfully. Beginning in 2011, the MTA installed "Help Point" to aid with emergency calls or station agent assistance, in all stations. Interactive touchscreen kiosks, which give station advisories, itineraries, and timetables, were installed starting in 2011. Cellular phone and wireless data in stations, first installed in 2011 as part of a pilot program, was expanded systemwide due to positive passenger feedback. Additionally, credit-card trials at several subway stations in 2006 and 2010 led to proposals for OMNY, a contactless payment system to replace the aging MetroCard system used to pay fares on MTA-operated transportation. Finally, in 2017, the MTA started installing digital advertisements in trains and stations.

Construction methods

When the IRT subway debuted in 1904, the typical tunnel construction method was cut-and-cover. The street was torn up to dig the tunnel below before being rebuilt from above. Traffic on the street above would be interrupted due to the digging up of the street. Temporary steel and wooden bridges carried surface traffic above the construction. The 7,700 workers who built the original subway lines were mostly immigrants living in Manhattan.

Contractors in this type of construction faced many obstacles, both natural and man-made. They had to deal with rock formations, and ground water, which required pumps. of sewers, as well as water and gas mains, electric conduits, and New York City steam system pipes had to be rerouted. Street railways had to be torn up to allow the work. The foundations of tall buildings often ran near the subway construction, and in some cases needed underpinning to ensure stability.

This method worked well for digging soft dirt and gravel near the street surface. However, tunnelling shields were required for deeper sections, such as the Harlem and East River tunnels, which used cast-iron tubes. Segments between 33rd and 42nd streets under Park Avenue, 116th Street and 120th Street under Broadway, and 145th Street and Dyckman Street (Fort George) under Broadway and Saint Nicholas Avenue as well as the tunnel from 96th Street to Central Park North–110th Street & Lenox Avenue, used either rock or concrete-lined tunnels.

About 40% of the subway system runs on surface or elevated tracks, including steel or cast iron elevated structures, concrete viaducts, embankments, open cuts and surface routes. All of these construction methods are completely grade-separated from road and pedestrian crossings, and most crossings of two subway tracks are grade-separated with flying junctions. The sole level junctions of two lines in regular revenue service are the 142nd Street junction and the Myrtle Avenue junction.

More recent projects use tunnel boring machines, which minimize disruption at street level and avoid already existing utilities, but increase cost. Examples of such projects include the extension of the IRT Flushing Line and the IND Second Avenue Line.

Automation and signaling

The MTA has plans to upgrade much of New York City Subway system from a fixed block signaling system to one with communications-based train control (CBTC) technology, which will control the speed and starting and stopping of subway trains. The CBTC system is mostly automated and uses a moving block system – which reduces headways between trains, increases train frequencies and capacities, and relays the trains' positions to a control room – rather than a fixed block system. This will require new rolling stock to be built for the subway system, as only newer trains can use CBTC systems.

Trains using CBTC locate themselves based on measuring their distance past fixed transponders installed between the rails. Trains equipped with CBTC have a transponder interrogator antenna beneath each carriage, which communicates with the fixed trackside transponders and report the trains' location to a wayside Zone Controller via radio. Then, the Controller issues Movement Authorities to the trains. This technology upgrade will allow trains to be operated at closer distances, slightly increasing capacity; will allow the MTA to keep track of trains in real time and provide more information to the public regarding train arrivals and delays; and will obviate the need for complex interlocking towers. The trains are also equipped with high-tech computers inside the cab so that the conductor could monitor the train's speed and relative location.

First two lines The BMT Canarsie Line () was the first line to implement the automated technology using Siemens's Trainguard MT CBTC system, as it was a self-contained line with none of the route interlining seen elsewhere around the system. The CBTC project was first proposed in 1994 and approved by the MTA in 1997. Installation of the signal system was begun in 2000. Initial testing began in 2004, and installation was mostly completed by December 2006, with all CBTC-equipped R143 subway cars in service by that date. Due to an unexpected ridership increase on the Canarsie Line, the MTA ordered more R160 cars and these were put into service in 2010. This enabled the agency to operate up to 26 trains per hour up from the May 2007 service level of 15 trains per hour, an achievement that would not be possible without the CBTC technology or a redesign of the previous automatic block signal system. The R143s and R160s both use Trainguard MT CBTC, supplied by Siemens.

The next line to have CBTC installed was the pre-existing IRT Flushing Line and its western extension opened in 2015 (served by the ). The Flushing Line was chosen for the second implementation of CBTC because it is also a self-contained line with no direct connections to other subway lines currently in use. The 2010–2014 capital budget provided funding for CBTC installation on the Flushing Line, with scheduled installation originally set for completion in 2016. The R188 cars were ordered in 2010 to equip the line with compatible rolling stock. This order consists of new cars and retrofits of existing R142A cars for CBTC. However, the CBTC retrofit date was later pushed back to 2017 or 2018. The installation is being done by Thales Group.

Expansion Siemens and Thales successfully conducted tests on one of the IND Culver Line's tracks to determine if their CBTC systems were compatible, thus allowing installation of CBTC on the rest of the B Division. In 2016, Siemens and Thales were awarded a contract to install CBTC on the IND Queens Boulevard Line from 50th Street/8th Avenue and 47th–50th Streets–Rockefeller Center to Kew Gardens–Union Turnpike. Planning for phase one started in 2015 and was complete by February 2016, with major engineering work following in November 2016.Install Communication-Based Train Control on the Queens Boulevard Line West – Phase 2 Funding for CBTC on the IND Eighth Avenue Line from 59th Street–Columbus Circle to High Street is also provided in the 2015–2019 Capital Program, along with the modernization of interlockings at 30th and 42nd Streets. The local tracks of the IND Culver Line would also get CBTC as part of the 2015–2019 Capital Program, as well as the entire line between Church Avenue and West Eighth Street–New York Aquarium, with three interlockings to be upgraded on that stretch.

, MTA projects that of track will receive CBTC signals by 2029, including most of the IND, as well as the IRT Lexington Avenue Line and the BMT Broadway Line. The MTA also is planning to install CBTC equipment on the IND Crosstown Line, the BMT Fourth Avenue Line and the BMT Brighton Line before 2025.

Additionally, the New York City Subway uses a system known as Automatic Train Supervision (ATS) for dispatching and train routing on the A Division (the Flushing line, and the trains used on the , do not have ATS.) ATS allows dispatchers in the Operations Control Center (OCC) to see where trains are in real time, and whether each individual train is running early or late. Dispatchers can hold trains for connections, re-route trains, or short-turn trains to provide better service when a disruption causes delays.

Other ideas In 2017, the MTA started testing ultra-wideband radio-enabled train signaling on the IND Culver Line. The ultra-wideband train signals would be able to carry more data wirelessly in a manner similar to CBTC, but can be installed faster. The ultra-wideband signals would have the added benefit of allowing passengers to use cellphones while between stations, instead of the current setup (see ) that only provides cellphone signals within the stations.

Platform screen doors

The MTA has long been reluctant to install platform screen doors in the subway system, though it had been considering such an idea since the 1980s. Originally, it was planned to install platform doors in several stations along the Second Avenue Subway and on the 7 Subway Extension, but their installation presented substantial technical challenges, as there are different placements of doors on New York City Subway rolling stock. The platform-door proposal was scrapped in 2012 because of high installation and maintenance costs, rolling stock door placement, the need to provide a suitable signal interface between the train and platform, and the potential delay in operations that would result from the operation of such doors.