thumb|right|300px|[[Train of Many Colors storage at 207th Street Yard]]
The New York City Transit Authority operates 24 rail yards for the New York City Subway system and one for the Staten Island Railway. There are 10 active A Division yards and 11 active B Division yards, two of which are shared between divisions for storage and car washing. In addition, there is one yard for the Staten Island Railway and three non-revenue (Maintenance of Way, or MoW) Division-independent yards. Many of the system's yards are used for off-peak storage, whereas some have inspection facilities where basic routine maintenance is carried out. Of these yards, rolling stock are assigned to seven A Division yards and seven B Division yards. Within the yards are 14 maintenance facilities, whereas two yards (207th Street and Coney Island) perform major overhaul and car rebuilding work.
A Division yards
The A Division's rail yards consist of the 239th Street, 240th Street, Corona, East 180th Street, Jerome, Livonia, and Westchester maintenance yards, plus three other non-maintenance storage yards. A total of 2,892 cars are assigned to the seven maintenance yards.
Cars in the A Division may be stored in B Division yards if necessary.
137th Street Yard
The 137th Street Yard is an underground storage yard located between 145th Street and 137th Street–City College on the IRT Broadway–Seventh Avenue Line, the latter of which is the yard's namesake. The yard is used to store some trains outside of rush hours. Each track can hold two full-length trains, so a total of ten trains can be stored there at any given time. Because the tracks are on a 1% downgrade in the southbound direction, each of the layup tracks are equipped with a derail to protect the main line from a runaway train in the event a train placed on any one the storage tracks is not properly secured.
239th Street Yard
thumb|239th Street Yard aerial view
thumb|left|239th Street Yard east side
left|thumb|An [[R142 (New York City Subway car)|R142 heading into the 239th St Yard, above several Redbirds and an R62A.]]
The 239th Street Yard is the northernmost rail yard in the system, located at 4570 Furman Avenue in the Wakefield section of the North Bronx, and is home to the R142s assigned to the . There is also considerable fleet interoperability with the , as 5 trains are based out of the nearby East 180th Street Yard and share a similarly sized fleet. 5 trains use the upper portion of the yard for off-peak storage. Opened in 1916, it is one of the oldest yards in the system.
Ten cars are inspected each day as part of preventative scheduled maintenance. A wheel truing machine was installed here to minimize damage to rail cars and tracks caused by flat wheels. This shop was also used as a facility to retrofit all R26s, R28s, R29s, R33s (except single unit Worlds Fair cars) and R36s (both Mainline and Worlds Fair types) married pairs IRT type cars with the installation of new Stone-Safety 10 ton Air Conditioning systems between 1976 and 1981. Also, during this period, all cars assigned to the were inspected and maintained at the East 180th Street Yard shared with the . It re-opened as an inspection and maintenance facility for the in 1982. A car wash operates at this yard facility to serve cars assigned to the 2, in addition to cars assigned to the , , and 5 routes.
The yard consists of a seven-track inspection shop and 38 layup tracks. The layup tracks are arranged on two levels; the only other yard in the system to share this trait is the East New York Yard. Access to the yard is provided to and from Nereid Avenue only.
240th Street Yard
thumb|240th Street Yard layup tracks
The 240th Street Yard is located at 5911 Broadway in the Riverdale section of the Bronx, serving the IRT Broadway–Seventh Avenue Line near the line's northern terminus. The yard consists of six inspection tracks in the shop and 15 additional layup tracks. The yard is home to the R62A subway cars assigned to the . The shop was built in 1906 to support the original IRT subway. Work constructing the yard and inspection shed was 60 percent complete in June 1910, and was estimated to be completed by January 1, 1911. The inspection shed went into service on May 1, 1911.
The yard and shops are entirely on an elevated structure. There is no car washer at this yard; trains usually go to be washed at the nearby 207th Street Yard and occasionally to the 239th Street or Westchester Yard. Ten cars undergo 10,000 mile SMS inspections per day, since their entire fleet has been unitized into five-car sets.
As part of the 2020–2024 Capital Plan, the shop will be rebuilt with more space in between track and the replacement of pits with elevated tracks.
Corona Yard
thumb|right|Corona Yard and shop
Corona Yard serves as the home yard of the IRT Flushing Line (). It is located south of Mets–Willets Point, at Flushing Meadows–Corona Park near Citi Field, the National Tennis Center, and the site of the 1939 and 1964 World's Fairs.
Corona Yard opened in 1928 and maintains the R188s used on the . It is adjacent to the Casey Stengel Bus Depot. Because the Flushing Line is isolated from the rest of the A Division and its only track connection to the rest of the system is via the B Division, cars that need to undergo or are returning from heavy maintenance are escorted on and off the line by suitably-equipped lead cars via the sole connection to the rest of the system just east (railroad north) of the upper level Queensboro Plaza station.
On August 16, 2006, the original 1928 shop building was demolished and replaced by a new, modern shop. With more track mileage to cover and tighter spacing between trains as part of CBTC implementation on the Flushing Line, the MTA announced plans to expand the yard with a second loop and six layup tracks, which would be located on the former right of way of the Long Island Rail Road's Whitestone Branch. Plans for this expansion are on an indefinite hold, however.
East 180th Street Yard
thumb|right|The East 180th Street Yard and Maintenance–Repair Shop; viewed from [[East 180th Street (IRT White Plains Road Line)|East 180th Street station]]
The East 180th Street Yard is situated at 1145 East 180th Street in the West Farms neighborhood of the Bronx, just east of the Bronx Zoo. The yard consists of seven storage tracks (numbered 4 thru 10) and an adjacent 6-track (numbered 11 thru 16) shop building with a connection to the nearby 19-track Unionport Yard, which lies to the northeast of East 180th Street Yard. Additionally, there are two storage tracks (identified as A and B) immediately north of the shop building. Track A ends in a bumper block and track B is accessible from the southbound track of the White Plains Road line. The yard is the home of the R142s for the . There is considerable fleet interchange with the . All engineering acceptance testing for newly delivered IRT-type cars is performed here. A new shop building replacing the original 1918 vintage shop building opened in 1999, just in time for acceptance testing of new R142s, which Bombardier started delivering to this facility on November 16, 1999. On October 11, 1923, additional tracks in the yard went into service.
Jerome Yard
The Jerome Yard, or Mosholu Yard, is located at 3191 Jerome Avenue in the Jerome Park neighborhood of the Bronx. The yard was built in 1925. Five tracks went into service in the yard on February 7, 1923.
This yard is home to the R142s and R142As for the . It is one of the three yards in the system to be under a housing complex (Pitkin Yard and Lenox Yard are the others). Rail access to the yard is by a pair of tracks that branch off of the elevated IRT Jerome Avenue Line just north of Bedford Park Boulevard–Lehman College station. The riveted steel pylons that support the elevated branch tracks give way to stone pylons just north of 205th Street before they enter the yard. The yard is surrounded by a wall and covered by a parking deck used by residents of the Tracey Towers housing complex. The yard has four inspection tracks, one utility track and 18 layup tracks. Trains are washed at the nearby Concourse Yard. is located near 148th Street and Lenox Avenue in Harlem. This 22 track yard is only used for storage of the R62s that operate on the , and has no maintenance facility, although the yard had been the first overhaul shop for the IRT when it opened with the rest of the new subway in 1904. The original IRT subway cars were lowered from the street via inclines into the yard, where they continued into the West Side Main Line. The inspection shed was lengthened to fit ten-car trains in Fiscal Year 1910. Formerly extending between 147th and 150th Streets, in the 1960s the yard was downsized from 26 acres to seven acres, which eliminated the repair shops and NYCT offices. The land was sold to a developer. Around that time, a public school building (currently housing Frederick Douglass Academy) and the Esplanade Gardens apartment complex were constructed on pilotis above the formerly open-air yard.
Livonia Yard
thumb|Northwest end of Livonia Yard
The Livonia Yard is located at 900 Hegeman Avenue in East New York, Brooklyn on an entirely elevated structure at the east end of the IRT New Lots Line. Located between Elton and Linwood Streets, the yard extends from Hegeman Avenue south to Stanley Avenue, passing over Linden Boulevard. One of the smallest maintenance yards in the system, it is where the R62s on the and the R62As on the 42nd Street Shuttle are inspected and maintained.
Additionally, a large amount of space within Livonia is used for the storage of some R142s and R142As for the , and trains.
Unionport Yard
thumb|Unionport Yard in 2019.
Unionport Yard is associated with the nearby East 180th Street Yard, and is used primarily as a lay-up facility for and trains. It is named after Unionport Road, which lies just east of the yard. There are no shop or wash facilities at this yard, which was expanded in the 1990s from five tracks to its present 19 (numbered 19 to 37). All but one track ends at bumper blocks. The newly expanded yard became fully operational in 1997. The yard connects to the IRT White Plains Road Line to the south and the IRT Dyre Avenue Line (track 22 connecting to track Y2) to the north. In addition to serving Manhattan Elevated Railway cars, it was also used to service cars assigned to the and routes.
Westchester Yard
thumb|Westchester Yard in 2023
The Westchester Yard, also known as the Pelham Yard, is located in the Bronx and has 45 layup tracks. The yard maintains and stores the R62As used on the , as well as Maintenance of Way diesel trains for both the A Division and B Division. It is connected to the IRT Pelham Line in both directions between Westchester Square–East Tremont Avenue and Middletown Road stations. Pelham Yard also has a car wash used by the entire A Division. The increased capacity of the yard allowed the yard to store 358 additional subway cars. With the additional storage space, it would no longer be required to lay up trains on the middle track of the line between East 177th Street and Pelham Bay Park, and it would allow for full day express service. The construction of substations would improve voltage conditions and allow for longer trains to be operated on the line. The work was projected to cost $6,387,000 and be completed in 1950.
B Division yards
The B Division's yards are the 207th Street, Concourse, Coney Island, East New York, Jamaica and Pitkin maintenance yards, plus five other non-maintenance storage yards. The six maintenance shops are responsible for performing daily subway car maintenance and inspection of 3,523 subway cars.
The 207th Street and Concourse yards are shared with the A Division and are listed in Yards in both divisions.
174th Street Yard
The 174th Street Yard is an underground rail yard on the IND Eighth Avenue Line that is used to store trains. The yard has five tracks to the east of the two mainline passenger service tracks. The yard is located six blocks north of 168th Street and adjacent to 175th Street. The inner tracks at 168th Street lead towards the yard and are used by terminating C trains.
Canarsie Yard
thumb|South end of Canarsie Yard
The Canarsie Yard (also known as AY or Atlantic Yard from its telegraphy letters) is located on the south end of the BMT Canarsie Line adjacent to Canarsie–Rockaway Parkway. Opened on October 26, 1917, it is the primary layup yard for the R143s and R160s on the and hosts the only car wash for the BMT Eastern Division.
New signals were installed in 2003 in conjunction with the BMT Canarsie Line automation project.
Coney Island Complex
thumb|Coney Island Complex
thumb|Inside view into a workshop
The Coney Island Rapid Transit Car Overhaul Shop, often shortened to Coney Island Complex, is the largest rapid transit yard in the state of New York, and one of the largest in North America.
Regular scheduled maintenance is performed here for a fleet of nearly 800 cars of R46s, R68s, R68As, R211As, and R211Ts serving the , , , , , and Franklin Avenue Shuttle. R68s on the , and R160s on the and , are stored at the yard but are not maintained or inspected here. The shop facility, along with the 207th Street Shops, performs inspections, heavy maintenance and overhaul for every one of the approximately 6,000 cars in the subway system, including the Staten Island Railway, and also contains car washing and painting facilities.