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Since the opening of the original New York City Subway line in 1904, and throughout the subway's history, various official and planning agencies have proposed numerous extensions to the subway system. The first major expansion of the subway system was the Dual Contracts, a set of agreements between the City of New York and the IRT and the BRT. The system was expanded into the outer reaches of the Bronx, Brooklyn, and Queens, and it provided for the construction of important lines in Manhattan. This one expansion of the system provided for a majority of today's system. Even with this expansion, there was a pressing need for growth. In 1922, Mayor John Hylan put out his plan for over 100 miles of new subway lines going to all five boroughs. His plan was intended to directly compete with the two private subway operators, the IRT and the BMT. This plan was never furthered. The next big plan, and arguably the most ambitious in the subway system's history, was the "Second System". The 1929 plan by the Independent Subway to construct new subway lines, the Second System would take over existing subway lines and railroad rights of way. This plan would have expanded service throughout the city with 100 miles of subway lines. A major component of the plan was the construction of the Second Avenue Subway. The Stock Market Crash of 1929 put a halt to the plan, however, and subway expansion was limited to lines already under construction by the IND. During the 1930s and 1940s, the plans were revised, with new plans such as a line to Staten Island and a revised line to the Rockaways. In the late 1940s and 1950s, a Queens Bypass line via the Long Island Rail Road's Main Line was first proposed as a branch of the still planned Second Avenue Subway. In addition, capacity on existing lines became improved through the construction of strategic connections such as the Culver Ramp, the 60th Street Tunnel Connection, and the Chrystie Street Connection, and through the rebuilding of DeKalb Avenue Junction. These improvements were the only things to come out of these plans. Eventually, these plans were modified to what became the Program for Action, which was put forth by the New York City Transit Authority in 1968. This was the last plan for a major expansion of the subway system. The plan included the construction of the Second Avenue Subway, a Queens Bypass line, a line replacing the Third Avenue El in the Bronx, and other extensions in the Bronx, Queens, and Brooklyn. While ambitious, very little of the plan was completed, mostly because of the financial crisis in the 1970s. Until the 1990s, there was little focus on expansion of the system because the system was in a state of disrepair, and funds were allocated to maintaining the existing system. In the 1990s, however, with the system in better shape, the construction of the Second Avenue Subway was looked into again. Construction of the Second Avenue Subway started in 2007, and the first phase was completed in 2017. Since the 1990s, public officials and organizations such as the Regional Plan Association have pushed for the further expansion of the system. Projects such as the TriboroRx, a circumferential line connecting the outer boroughs, the reuse of the Rockaway Beach Branch, and the further expansion of the Second Avenue Subway have all been proposed, albeit mostly unfunded.

The Triborough System was a proclamation for new subway lines to the Bronx and Brooklyn. The new lines include the IRT Lexington Avenue Line, IRT Pelham Line, and IRT Jerome Avenue Line. The Manhattan Bridge line described below later became the BMT West End Line, BMT Fourth Avenue Line, the BMT Sea Beach Line, and the Nassau Street loops. The route of the new subway  comprises a main trunk north and south through Manhattan Borough on Lexington Avenue and Irving Place from the Harlem River to Tenth St. and on Broadway, Vesey and Church Sts. from Tenth St. to the Battery; two branches in Bronx Borough, one northeast via 138th St. Southern Boulevard and Westchester Ave. to Pelham Bay Park. the other northerly via River Ave. and Jerome Ave. to Woodlawn Road, connecting with the Manhattan trunk by a tunnel under the Harlem River; a Manhattan Brooklyn line extending from the North River via Canal Street across the East River on the Manhattan Bridge to connect with the Fourth Avenue subway in Brooklyn now being built, which thus becomes an integral part of the larger system; two branches southerly from the Fourth Ave. line extending south to Fort Hamilton and southeast to Coney Island; and a loop feeder line in Brooklyn through Lafayette Ave. and Broadway, connecting with the Fourth Ave. line at one end. and at the other crossing the Williamsburg Bridge and entering the Centre Street Loop subway in Manhattan which is thus also incorporated in the system. In 1911, William Gibbs McAdoo, who operated a competing subway company called the Hudson & Manhattan Railroad, proposed building a line under Broadway between Hudson Terminal and Herald Square. He later proposed that the Broadway line be tied into the IRT's original subway line in Lower Manhattan. The Broadway line, going southbound, would merge with the local tracks of the IRT Lexington Avenue Line in the southbound direction at 10th Street. A spur off the Lexington Avenue Line in Lower Manhattan, in the back of Trinity Church, would split eastward under Wall Street, cross the East River to Brooklyn, then head down the Fourth Avenue Line in Brooklyn, with another spur underneath Lafayette Avenue. The Triborough System later became part of the Dual Contracts, signed on March 19, 1913 and also known as the Dual Subway System. These were contracts for the construction and/or rehabilitation and operation of rapid transit lines in New York City. The contracts were "dual", in that they were signed between the City and the IRT and Municipal Railway Company, a subsidiary of the BRT (later BMT). Some lines proposed under the Contracts were not built, most notably an IRT line to Marine Park, Brooklyn (at what is now Kings Plaza) under either Utica Avenue, using a brand new line, or Nostrand Avenue and Flatbush Avenue, using the then new IRT Nostrand Avenue Line. There were also alternate plans for the Nostrand Avenue Line to continue down Nostrand Avenue to Sheepshead Bay.

Before unification in 1940, the government of New York City made plans for expanding the subway system, under a plan referred to in contemporary newspaper articles as the IND Second System (due to the fact that most of the expansion was to include new IND lines, as opposed to BMT/IRT lines). The first one, conceived in 1929, was to be part of the city operated Independent Subway System (IND). By 1939, with unification planned, all three systems were included. Very few of these far reaching lines were built, though provisions were made for future expansion on lines that intersect the proposals. Cost is only for construction, and does not include land acquisition or other items. LineStreetsFromToTracksRoute milesTrack milesCostNotesManhattanEast Manhattan trunk line (Second Avenue Line)Water Street – New Bowery – Chrystie StreetPine StreetHouston Street2 from Pine Street to Chambers Street4 to Houston Street1.344.68$11,300,000subwaySecond AvenueHouston StreetHarlem River4 to 61st Street6 to 125th Street4 to Harlem River6.5532.84$87,600,000subway61st Street LineSixth Avenue – 61st Street52nd StreetSecond Avenue21.12.2$6,700,000subway(Rockaway Line)Worth Street – East Broadway – Grand StreetChurch StreetEast River21.953.9$13,300,000subway(Utica Avenue Line)Houston StreetEssex StreetEast River2.931.86$7,900,000subwayManhattan subtotal11.8745.48$126,800,000BronxBronx trunk lineAlexander Avenue – Melrose Avenue – Boston RoadHarlem RiverWest Farms43.9715.88$40,400,000subway, with a portal between Vyse Avenue and 177th Street, then elevated into the existing IRT White Plains Road Line near 180th StreetWhite Plains Road LineMorris Park Avenue – Wilson AvenueGarfield StreetBoston Road23.57.9$13,700,000branching off the existing elevated IRT White Plains Road Line, and then going into subwayIRT Lafayette Avenue Line163rd Street – Hunts Point – Lafayette Avenue – 177th StreetWashington Avenue at Brook AvenueEast Tremont Avenue25.0210.04$12,900,000subway to near Edgewater Road and Seneca Avenue, then elevatedConcourse Line ExtensionBurke Avenue – Boston RoadWebster AvenueBaychester Avenue22.154.3$8,900,000extension of the Concourse LineWhite Plains Road Line 180th Street241st Street 4.4013.2$2,100,000owned by IRT, to be taken over ("recaptured") by INDBronx subtotal19.0451.32$77,000,000BrooklynBroadway Branch Line (Rockaway Line)BroadwayEast RiverHavemeyer Street at South Fourth Street23.1613.5$34,800,000subwayUtica Avenue Line (and Rockaway Line from Havemeyer Street to Stuyvesant Avenue)Grand Street – South Fourth Street – Beaver StreetEast RiverStuyvesant Avenue2 to Driggs Avenue4 to Union Avenue8 to Bushwick Avenue4 to Stuyvesant AvenuesubwayStuyvesant Avenue – Utica AvenueBroadwayFlatbush Avenue45.8523.4$39,300,000subway to Avenue J, then elevatedAvenue SUtica AvenueNostrand Avenue21.12.2$2,000,000elevatedNostrand AvenueAvenue SVoorhies Avenue41.35.2$3,200,000elevatedRockaway LineMyrtle AvenueBushwick AvenuePalmetto Avenue41.345.36$14,300,000subwayFulton Street LineLiberty AvenueFulton Street and Eastern ParkwayGrant Avenue41.847.36$13,500,000subway extending the Fulton Street Line to a portal at Liberty Avenue and Crescent Street, then elevated to connect to the BMT Liberty Avenue Line (now part of the Fulton Street Line) at Grant AvenueNostrand Avenue Extension Flatbush AvenueAvenue S22.254.5$7,400,000Extension of Nostrand Avenue Line as subway to Kings Highway, then elevatedBrooklyn subtotal16.8461.52$114,500,000QueensRockaway LineMyrtle Avenue – Central AvenuePalmetto Avenue78th Street42.18.4$17,300,000subway to Central Avenue near 73rd Place, then along the surface or elevated98th Street – 99th Street – Hawtree Street78th StreetHammels Station4 to Howard Beach2 to Hammels9.226.2$20,200,000along the surface or elevatedRockaway Beach BoulevardBeach 116th StreetMott Avenue25.010.0$7,400,000along the surface or elevatedNewport Avenue Line(Rockaway Line Extension)Newport AvenueBeach 116th StreetBeach 149th Street21.63.2$2,400,000along the surface or elevatedWinfield SpurGarfield Avenue – 65th Place – Fresh Pond RoadBroadway and 78th StreetCentral Avenue23.346.68$10,100,000subway to 45th Avenue, then elevated to Fresh Pond Road, then subway;terminal station partially built as part of Roosevelt Avenue Jackson Heights station, with short trackways leading to the spur. Brinckerhoff Hollis Avenue Line(Fulton Street Line Extension)Liberty Avenue – 105th Avenue – Brinckerhoff Avenue – Hollis AvenueLefferts BoulevardSpringfield Boulevard26.213.3$10,700,000elevated extension of the BMT Liberty Avenue Line (now part of the Fulton Street Line)includes branch connection to BMT Jamaica Line (BMT) at 168th Street, via 180th Street and Jamaica AvenueVan Wyck Boulevard Line137th Street – Van Wyck Boulevard87th AvenueRockaway Boulevard22.34.6$6,600,000subway to about 116th Avenue, then elevated120th Avenue Line120th Avenue – Springfield BoulevardHawtree Street near North Conduit BoulevardFoch Boulevard(now Linden Boulevard)4 to Van Wyck Boulevard2 to Foch Boulevard5.2313.92$9,500,000elevatedBayside LineRoosevelt Avenue – First Street – Station Road – 38th AvenueMain Street221st Street3 to 147th Street2 to 221st Street3.67.78$9,600,000extends the BMT/IRT Flushing Line as a subway to 155th Street, then elevatedCollege Point and Whitestone Line149th Street – 11th AvenueRoosevelt Avenue and 147th Street11th Avenue and 122nd Street23.46.8$6,000,000subway to 35th Avenue, then elevatedLong Island City Horace Harding Boulevard LineDitmars Avenue – Astoria Boulevard – 112th Street – Nassau Boulevard (Long Island Expressway)Second AvenueCross Island Boulevard2 to Astoria Boulevard4 to Parsons Boulevard2 to Cross Island Boulevard8.126.71$17,700,000extends the BMT/IRT Astoria Line as an elevated, except that part of it may be depressed near Nassau Boulevard (Long Island Expressway)Liberty Avenue Line Grant AvenueLefferts Boulevard32.36.9$1,600,000owned by BMT, to be taken over ("recaptured") by INDnow part of the Fulton Street LineQueens subtotal52.37136.49$119,100,000Total100.12294.81$438,400,000

The IND expansion plan was revised in 1932. It differs from the 1929 plan, but there are , of which 12.49 mile (20 km) are in Manhattan, 12.09 mile (19 km) in the Bronx, 13.14 mile (21 km) in Brooklyn, and 23.21 mile (37 km) in Queens. It would include a new 34th Street crosstown line, a Second Avenue Subway line, a connection to the New York, Westchester and Boston Railway, and extensions of the IRT Nostrand Avenue Line, IRT Flushing Line, and BMT Astoria Line. It would have created a subway loop bounded by 2nd and 10th Avenues, and 34th and 125th Streets. This plan included no extensions to Whitestone, Queens, however, with the plan to instead serve more densely populated areas such as Astoria and the Roosevelt Avenue corridor. The plan would also take over the local tracks of the New York, Westchester and Boston Railway, and the Rockaway Beach Branch of the Long Island Rail Road. (1939 plan) A line splitting from the South Brooklyn (Culver) Line at Fort Hamilton Parkway or Church Avenue, and running under Fort Hamilton Parkway to 86th Street. A branch would split to run under Ovington Avenue and Senator Street, with a tunnel under the Narrows to Staten Island at the St. George Terminal. The line would split, with the north branch ending at Westervelt Avenue around Hamilton Avenue, and the south branch ending at Grant Street around St. Pauls Street. It was presumably designed this way to provide future service to both the Main Line and North Shore Staten Island Railway lines. The Staten Island Tunnel commenced construction in 1923 to serve the BMT Fourth Avenue Line, but was not completed. (1940 plan, revised 1945) The IND Fulton Street Line would connect to what is now the IND Rockaway Line. A branch of the IND Fulton Street Line would run to a stub end terminal at 105th Street. The line, east of Euclid Avenue, would be 4 tracks until Cross Bay Boulevard, where the two branches would split. (unknown date) A third 2 track tunnel under the East River, from the north side of the South Fourth Street/Union Avenue station (as built for six tracks) west to Delancey Street. (unknown date) A line splitting from the Stuyvesant Avenue line, going southeast under Broadway. (unknown date) A line under Flushing Avenue from the huge line under Beaver Street to Horace Harding Boulevard (Long Island Expressway). (unknown date) A 4 track subway under Bedford Ave in Brooklyn connecting to the Worth St Subway and 2nd Ave Subway. An earlier plan in 1920 had an even more expansive plan, with several dozen subway lines going across all five boroughs.

After World War II and up until the late 1990s, the New York City Subway did not expand much. Only 28 stations opened in that time, compared to the remaining 393 stations, which opened from the 1880s to before World War II. As such, there have been many plans to expand the system during this time period.

In 1986, the Regional Plan Association suggested extending the IRT Flushing Line across the Hudson River to the Meadowlands Sports Complex in East Rutherford, New Jersey. In 1986, the MTA issued a study on expanding transit options on the west side of Manhattan. It was proposed to use the West Side Line viaduct (today's High Line), and various means of transportation were proposed, including monorail, passenger rail trains, or subway trains. It also proposed to extend the IRT Flushing or BMT Canarsie Lines ( and , respectively).

In 1990, the MTA proposed a rail line connecting LaGuardia Airport and John F. Kennedy International Airport. The line would have operated over the Grand Central Parkway and the Van Wyck Expressway. There would be stations at Shea Stadium and Jamaica. The system was proposed to cost $2billion. The MTA estimated that the rail link would take 30minutes from Kennedy to LaGuardia, and the frequency of service would initially be every 15minutes. There would be a two track alignment with one track for each direction, as well as at least two trains heading in each direction at all times. If the link were built, the average travel time from Manhattan to Kennedy would have been about 45minutes using the Long Island Rail Road, including transfers. To LaGuardia, the average travel time from the Grand Central station using the IRT Flushing Line would be 47minutes.

In mid October 2019, the MTA announced that it would study the feasibility of restoring passenger service on the Bay Ridge Branch portion of the route. In early January 2022, as part of her State of the State address New York governor Kathy Hochul announced that the state would move forward with the Bay Ridge Branch Line by conducting an environmental study on the Interborough Express (IBX), a 14 mile (23 km) corridor using the existing Bay Ridge Branch and Fremont Secondary from Bay Ridge, Brooklyn, to Jackson Heights, Queens. End to end travel times are expected to be less than 40 minutes, and weekday ridership is projected to be 115,000. The route would connect up to 17 subway lines and the Long Island Rail Road. The MTA indicated in September 2022 that it wanted to construct the IBX as a light rail line, and Hochul announced in January 2023 that the project would proceed as a light rail corridor.

The Long Island Rail Road (LIRR) abandoned the Rockaway Beach Branch in 1962; ever since it has been sought after for reactivation for train service. The line has not been reactivated due to local opposition, specifically the homeowners who live along the right of way. One group, QueensLink, wants the line to be reactivated between the 63rd Drive–Rego Park station on the IND Queens Boulevard Line to the north and the IND Rockaway Line to the south, providing a north south connection in Queens. A second group would use the right of way as a linear park, known as the Queensway, a proposal inspired by the success of the High Line in Manhattan. A third group consists of homeowners who would have nothing done, keeping the line as is. Talks of reactivating the line were publicly endorsed in February 2012 by Assemblymen Phillip Goldfeder and Michael G. Miller. Goldfeder commented "The commute for people here is only going to go from bad to worse. You can't talk about a convention center without talking about transportation." Goldfeder and Miller said they are not opposed to turning sections of the line into a park, but said people who live in the Rockaways, Ozone Park and other areas have no quick or easy way to get into Manhattan. The Genting Group, which operates Resorts World casino and have been asked to construct the convention center, are evaluating several plans to increase transportation access. Genting is committed to paying for part of the transportation improvements. Advocates of the Queensway, a proposed public park along the branch's route, are against resumption of rail service, stating that current bus service fills current transportation needs in the area. U. S. Representatives Hakeem Jeffries and Gregory Meeks added their support for the project in March 2013. Both representatives will push to allocate federal transportation subsidies to study a plan for restored passenger service. The line would cost $1 billion, if build in its full length with a connection to the IND Queens Boulevard Line, and would stretch across 3.5 mile (6 km), providing connections to several subway services as well as the LIRR. Another possible option would have Long Island Rail Road service restored with service to seven stations along the right of way, with service ending in Howard Beach. The line would serve upwards of 250,000 passengers per day and would provide access to JFK Airport from Midtown Manhattan. In February 2015, the Regional Plan Association suggested having some F trains, after running through the 63rd Street Tunnel, be rerouted to operate over the Lower Montauk Branch of the LIRR running through underserved Maspeth and Glendale and then meeting up with the Rockaway Beach Branch in Rego Park. The New York Daily News editorial board came out in support of this extension on February 21, 2017, detailing why this route is superior to Governor Andrew Cuomo’s plan for an AirTrain from LaGuardia to Willets Point.

In April 2015, New York City Mayor Bill de Blasio announced a new plan for building a subway line under Utica Avenue in Brooklyn. Previous plans, most recently the Program for Action, had provisions for such a line. It would branch off from the IRT Eastern Parkway Line at Crown Heights–Utica Avenue. The new line being proposed is part of de Blasio's "One New York" plan, which aims to improve transit, reduce emissions, and fight poverty. If built, the line would go to Flatbush Avenue, near Kings Plaza. Since the Metropolitan Transportation Authority had budget shortages as of April 2015, however, it is unclear how the line would be funded or built. The MTA Board allocated $5 million for a feasibility study, the Utica Avenue Subway Extension Study, for this proposal in the MTA's 2015–2019 Capital Program. In August 2016, it was reported that the MTA was looking into an extension of the IRT Nostrand Avenue Line along Flatbush Avenue to Marine Park, which would allow trains to serve Kings Plaza. Both the Utica Avenue and Nostrand Avenue proposals for extensions to Kings Plaza have been proposed since the 1910s. because it was no longer viewed as a priority by the MTA. Planning resumed in April 2019 when New York City Transit joined city agencies in launching the Utica Avenue Transit Improvement Study. The study will look into a subway extension, improved bus rapid transit, and a new light rail line. Since the study occurred concurrently with the 2020 redesign of Brooklyn bus routes, the MTA decided to prioritize the Utica Avenue transit study. In November 2017, the RPA suggested building both lines as part of its fourth plan. The Nostrand Line was envisioned as a three stop extension to Avenue Z, while the Utica Line was planned as a five stop spur to Kings Plaza. Under the RPA's plan, the Second Avenue Subway would be completed to its full length within Manhattan and then extended to the Bronx. The 7 Subway Extension would expand in scope, with the IRT Flushing Line being extended to 14th Street and Eighth Avenue. Ultimately, the plan included eight extensions with at least 40 stations in total. as of 2022, a potential extension of the BMT Broadway Line to Red Hook (to be served by the W train) is being evaluated as part of the MTA's 2025–2044 20 Year Needs Assessment.

as of 2022, a potential extension of the IRT New Lots Line (to be served by the 3 train) to Spring Creek, Brooklyn, is being evaluated as part of the 2025–2044 20 Year Needs Assessment.