Long Island Rail Road

A map of diesel territory on the Long Island Rail Road

• The Main Line runs from Long Island City east to Greenport. It is electrified west of the Ronkonkoma station; limited diesel train service runs from this point to the Yaphank, Riverhead, or Greenport stations. Trains using the East River Tunnels from Penn Station join the line at Sunnyside Yard. The services that run along this line are named after the branches they use; trains beyond Hicksville, where the Port Jefferson Branch diverges, are known as Ronkonkoma Branch and Greenport Branch trains.
• The Montauk Branch runs from Long Island City east to the Montauk station, with junctions with the Main Line at Long Island City and Jamaica. It is electrified from Jamaica east to Babylon. Trains operating east of Babylon are listed as Montauk Branch service and are hauled by diesel locomotives, while trains using the line from Jamaica to Babylon are labeled as Babylon Branch trains. The portion of the line between Long Island City and Jamaica, known as the Lower Montauk Branch, no longer carries passenger trains and is used only for freight service.
• The electrified Atlantic Branch runs from Atlantic Terminal in Downtown Brooklyn east to Jamaica, where it meets the Main Line and the Montauk Branch, and then heads southeast to become the Long Beach Branch east of Valley Stream. East of Valley Stream, the Far Rockaway Branch turns south, while the West Hempstead Branch turns northward.
• The electrified Port Washington Branch, the only one that does not serve Jamaica, branches from the Main Line west of Woodside (running parallel to the Main Line until Winfield Junction, which is east of that station) and runs east to Port Washington. It only serves four stations in Nassau County. It contains the Manhasset Viaduct, which is the highest bridge on the LIRR network.[30]
• The Port Jefferson Branch splits from the Main Line east of Hicksville, with electric service to Huntington and diesel service to Port Jefferson. Until 1938, it continued east to Wading River.[31]^: 258
• The electrified Hempstead Branch splits from the Main Line east of Elmont (running parallel to the Main Line until just after Floral Park) and runs east to Hempstead. At Garden City, the Garden City-Mitchel Field Secondary curves off and goes to Mitchel Field.
• The electrified West Hempstead Branch splits from the Montauk Branch east of the Valley Stream station and runs northeast to West Hempstead, originally continuing to junctions with the Hempstead Branch and the Oyster Bay Branch at the Main Line.
• The Oyster Bay Branch splits from the Main Line east of Mineola and heads north and east to Oyster Bay. The first section to East Williston is electrified;[32] only diesel trains run along the majority of the line to Oyster Bay.[33]
• The diesel-only Central Branch runs southeast from the Main Line east of Bethpage to the Montauk Branch west of the Babylon station, giving an alternate route to the Montauk Branch east of Babylon. The Central Branch used to continue west from Bethpage to include what is now the Garden City–Mitchel Field Secondary. It is to be electrified as part of the 2020–2024 MTA Capital Program.[34]
• The electrified Far Rockaway Branch splits from the Atlantic Branch east of the Valley Stream station and runs south and southwest to Far Rockaway. It used to connect westward to what is now the New York City Subway's IND Rockaway Line to the Hammels and Rockaway Park neighborhoods of Queens.
• The electrified Long Beach Branch begins where the Atlantic Branch ends east of the Valley Stream station (running parallel to the Montauk Branch until just after Lynbrook) where it turns south to end at Long Beach.

The railroad has dropped a number of branches due to lack of ridership over the years. Part of the Rockaway Beach Branch became part of the IND Rockaway Line of the New York City Subway, while others were downgraded to freight branches, and the rest abandoned entirely. Additionally, the Long Island Rail Road operated trains over portions of the Brooklyn Rapid Transit (BRT) elevated and subway lines until 1917.[35]

• The Bethpage Branch ran north from the Main Line and Central Branch at Bethpage.[36]
• The Bushwick Branch, also called the Bushwick Lead Track, is a freight railroad branch that runs from Bushwick, Brooklyn, to Fresh Pond Junction in Queens, where it connects with the Montauk Branch.
• The Camp Upton Branch was a short branch north from the Main Line to Camp Upton.[37]
• The Cedarhurst Cut-off, officially known as the New York and Rockaway Railroad, was an extension of the Montauk Branch from its merger with the Atlantic Branch at Springfield Junction to Cedarhurst, where it would turn west and run parallel to the Far Rockaway Branch until reaching Mott Avenue in Far Rockaway.
• The Central Extension ran from Garden City eastward to Central Park (¾ mile south of current Bethpage station) and as far east as Bethpage Junction. The line was cut back to the point where it stopped at Island Trees. Today the western part of track still in use for freight and storage, and is officially known today as the Garden City Secondary.
• The Chestnut Street Incline (Brooklyn) between Atlantic Avenue and Fulton Street was opened in 1898 to allow for thru-operation over the Jamaica/Broadway Elevated Line to the East River ferry terminal. In 1909 thru passenger service to Manhattan via the Williamsburg Bridge was established in coordination with the Brooklyn Rapid Transit Company (BRT). LIRR Passenger service operated to Chambers Street between May 1909 and September 1917.
• The Creedmoor Branch, a remnant of the Central Railroad of Long Island (CRRLI) of Alexander Turney Stewart, was a short branch from the Main Line at Floral Park northwest through Creedmoor. It once went as far northwest as Flushing.
• The Evergreen Branch connected the Bushwick Branch east of Bushwick Terminal with the Bay Ridge Branch north of East New York.
• The Flushing Bay Freight Spur extended north from the Whitestone Branch, then across the Woodside Branch and then the connecting line between both branches before terminating along the south coast of Flushing Bay.[38]
• The Glendale Cut-off ran south from the Main Line at Rego Park to the Montauk Branch at Glendale. There it became the Rockaway Beach Branch, running south across Jamaica Bay to Hammels and west to Rockaway Park. The Rockaway Beach Branch south of Ozone Park is now the IND Rockaway Line of the New York City Subway.
• The Manhattan Beach Branch ran south from the Bay Ridge Branch at Flatbush to Manhattan Beach.
• The Manorville Branch or Manor Branch ran from the Main Line at Manorville southeast to the Montauk Branch at Eastport. It was originally part of the Sag Harbor Branch (See below).
• The Mineola-West Hempstead Branch ran north of the terminus of the West Hempstead Branch across NY 24 to Country Life Press Station where it briefly joined the Hempstead Branch then ran north of the Garden City Secondary towards a wye at Mineola Station with one branch that terminated at the station and another that crossed the main line and ended near the southern terminus of the Oyster Bay Branch.
• The Montauk Cut-off was a short connecting track between the Lower Montauk Branch and the Main Line in Long Island City that allowed trains to change direction without entering the Long Island City station.[39]
• The Northport Branch ran northeast of the current Port Jefferson Branch between Greenlawn and Northport Village.[40]
• The North Shore Freight Branch ran from the Main Line at Sunnyside Yard west to the East River where Gantry Plaza State Park is now.[41][42] Originally built by the Flushing and North Side Railroad, some of the surviving right-of-way can be found at the Arch Street Shops within the Sunnyside Yard.
• The Roosevelt Field Spur branched off northward from the current Garden City Secondary just north of Commercial Avenue. From there, it crossed Stewart Avenue just west of present-day South Street before turning slightly northeast, crossing over the Meadowbrook Parkway. The overpass, as well as sections along the sidewalk on South Street, can still be seen today. From there, it continued north before curving east and coming to an end near Zeckendorf Boulevard. The line was used for freight only.
• The Sag Harbor Branch ran north from the Montauk Branch at Bridgehampton to Sag Harbor.
• The Wading River Branch ran east from Port Jefferson to Wading River, serving the towns of Mount Sinai, Miller Place, Rocky Point, and Shoreham.[43]
• The White Line, which was built by the LIRR subsidiary Newtown and Flushing Railroad ran south of the Port Washington Branch between Winfield Junction and Flushing between 1873 and 1876.[44]
• The Whitestone Branch, which was originally built by the Flushing and North Side Railroad (F&NS), split from the Port Washington Branch near Mets–Willets Point station and ran north and east to Whitestone.
• The Woodside Branch ran north of the current Port Washington Branch between Woodside and east of the present Corona Yard west of the Flushing River. It also had a connecting spur to the Whitestone Branch.

The Mets-Willets Point station.

In addition to its daily commuter patronage, the LIRR also offers the following services:

• From April to October, the railroad adds stops at Mets–Willets Point station to trains on the Port Washington Branch to serve passengers traveling to see New York Mets home games at Citi Field and the US Open at the USTA Billie Jean King National Tennis Center. When the number of passengers requires it, additional trains may be added.[45]
• The railroad operates extra trains during the summer season that cater to the Long Island beach trade. Special package ticket deals are offered to places like Long Beach, Jones Beach, the Hamptons, Montauk, and Greenport. Some of these packages require bus and ferry connections.
• The railroad operates extra trains to and from Atlantic Terminal for Brooklyn Nets home games at Barclays Center.[46]
• From May through October, the railroad runs four daily trains to Belmont Park (two in each direction) during the racetrack's summer meets. Additionally, on the day of the Belmont Stakes horse race the railroad runs extra trains to accommodate the large number of spectators attending the event.[47]
• One special non-passenger service offered by the railroad was the yearly operation of the Ringling Brothers Barnum and Bailey Circus train between Long Island City and Nassau Veterans Memorial Coliseum in Uniondale. Highly publicized by the LIRR, this event drew large crowds of spectators.[48] With Ringling Bros. Barnum and Bailey's closure, this was discontinued in May 2017.

The Mineola Intermodal Center (bottom left), as seen prior to the commencement of the construction on the Main Line's third track.

Penn Station offers connections with Amtrak intercity trains and NJ Transit commuter trains, as well as the PATH, New York City Subway, and New York City Bus systems.[49] Grand Central offers connections with Metro-North Railroad, as well as the subway and bus systems. Additionally, almost all stations in Brooklyn and Queens offer connections with the New York City Bus system, and several stations also have transfers to New York City Subway stations.[50] Transfers to Nassau Inter-County Express and Suffolk County Transit buses are available at many stations in Nassau and Suffolk counties, respectively.[51][52]

Peak fares are charged during the week on trains that arrive at western terminals between 6 AM and 10 AM, and for trains that depart from western terminals between 4 PM and 8 PM.[55] Any passenger holding an off-peak ticket on a peak train is required to pay a step up fee.[56] Passengers can buy tickets from ticket agents or ticket vending machines (TVMs) or on the train from conductors, but will incur an on-board penalty fee for doing so.[56] This fee is waived for customers boarding at a station without a ticket office or ticket machine, senior citizens, people with disabilities or Medicare customers.[56]

There are several types of tickets: one way, round trip, peak, off-peak, AM peak or off-peak senior/disabled, peak child, and off-peak child. On off-peak trains, passengers can buy a family ticket for children who are accompanied by an 18-year-old for $0.75 if bought from the station agent or TVM, $1.00 on the train. Senior citizen/disabled passengers traveling during the morning peak hours are required to pay the AM peak senior citizen/disabled rate. This rate is not charged during PM peak hours.[57]

Commuters can also buy a peak or off-peak ten trip ride, a weekly unlimited or an unlimited monthly pass.[58] Monthly passes are good on any train regardless of the time of day, within the fare zones specified on the pass.[58]

The LIRR charged off-peak fares at all times during the COVID-19 pandemic.[59] Peak fares were reinstated on March 1, 2022, and several new discounts and ticket options were introduced at the same time.[60]

During the summer the railroad offers special summer package ticket deals to places such as Long Beach, Jones Beach, the Hamptons, Montauk, and Greenport. Passengers traveling to the Hamptons and Montauk on the Cannonball can reserve a seat in the all-reserved Parlor Cars.[61]

Prior to November 2021, passengers going to Belmont Park had to buy a special ticket to go from Jamaica to Belmont Park (or vice versa). Weekly and monthly passes were not accepted at Belmont Park.[62] With the opening of Elmont station in November 2021, Belmont Park and Elmont were placed into fare zone 4.[63]

In 2003, the LIRR and Metro-North started a pilot program in which passengers traveling within New York City were allowed to buy one-way tickets for $2.50.[64] The special reduced-fare CityTicket, proposed by the New York City Transit Riders Council,[64] was formally introduced in 2004.[65] The discounted fares were initially only available for travel on Saturdays and Sundays.[66] In March 2022, it was expanded to include all off-peak trains throughout the week for $5.[67] The MTA announced plans in December 2022 to allow CityTickets to be used on peak trains as well;[68][69] governor Kathy Hochul confirmed these plans the next month.[70] The peak CityTickets, as announced in July 2023, would cost $7 each.[71]

CityTicket is valid for travel within zones 1 and 3 on the Long Island Railroad. CityTickets can only be bought before boarding, except at Willets Point where they can be purchased on board, and they must be used on the day of purchase.[62] CityTicket was originally not valid for travel to Far Rockaway because the station is in Zone 4 (despite being within the city limits) and the Far Rockaway Branch passes through Nassau County.[62][72] In May 2023, MTA officials announced that they would expand CityTicket to Far Rockaway.[73][74] CityTicket is also not valid for travel to the Elmont station or the special event only Belmont Park station, which are just barely east of the Queens-Nassau border and thus are within Zone 4.[62]

In late 2017, the MTA was slated to launch a pilot that will allow LIRR, bus and subway service to use one ticket.[75] The proposal for the ticket, called the "Freedom Ticket," was initially put forth by the New York City Transit Riders Council (NYCTRC) in 2007.[76]^: 1 The NYCTRC wrote a proof of concept report in 2015.[77] At the time of the report, express bus riders from Southeast Queens had some of the longest commutes in the city, with their commutes being 96 minutes long, yet they paid a premium fare of $6.50.[76]

Riders who take the dollar van to the subway paid $4.75 to get to Manhattan in 65 minutes; riders who only took the bus and subway paid $2.75 to get to Manhattan in 86 minutes; and riders who took the LIRR paid $10 to get to Manhattan in 35 minutes.[76]^: iii Unlike the CityTicket, the Freedom Ticket would be valid for off-peak and multidirectional travel; have free transfers to the subway and bus system; and be capped at $215 per month.[76]^: 1–2 At the time, monthly CityTickets cost $330 per month.[77]

The Freedom Ticket will initially be available for sale at the Atlantic Terminal, Nostrand Avenue, and East New York stations in Brooklyn and at the Laurelton, Locust Manor, Rosedale, and St. Albans stations in Queens.[75][78][79] Riders, under the pilot, would be able to purchase one-way, weekly, or monthly passes that will be valid on the LIRR, on buses, and the subway. The fare will be higher than the price of a ride on the MetroCard, but it will be lower than the combined price of an LIRR ticket and a MetroCard, and it will allow unlimited free transfers between the LIRR, buses, and subway.[79]

The former head of the MTA, Thomas Prendergast, announced at the January 2017 board meeting that the plan would be explored in a field study to determine fares and the impact on existing service.[75] The plan is intended to fill approximately 20,000 unused seats of existing trains to Atlantic Terminal and Penn Station (or about 50% to 60% of peak trains in each direction),[78] while at the same time providing affordable service to people with long commutes.[79] The details were to be announced in spring 2017, and the pilot would last six months.[75]

The MTA Board voted to approve a six-month pilot for a similar concept, the Atlantic Ticket, in May 2018. The Atlantic Ticket is similar in that it would allow LIRR riders in southeast Queens to purchase a one-way ticket to or from Atlantic Terminal for $5. The Atlantic Ticket would start in June 2018.[80] The success of the pilot program has led the MTA to extend the program up to the summer of 2020 and renewed calls for the program to be implemented within New York City, where the fare for the Freedom Ticket—if approved—would cost US$2.75 and include free transfers between the LIRR & Metro-North, bus, and subway.[81]

In 2017, it was announced that the MetroCard fare payment system, used on New York City-area rapid transit and bus systems, would be phased out and replaced by OMNY, a contactless fare payment system. Fare payment would be made using Apple Pay, Google Pay, debit/credit cards with near-field communication enabled, or radio-frequency identification cards.[82][83] As part of the implementation of OMNY, the MTA also plans to use the system in the Long Island Rail Road and Metro-North Railroad.[84]

On December 2022, the MTA announced the launch of an additional fare for use on journeys that utilize both of its railroad systems via Grand Central. The fare is priced as $8 more than an adult off-peak ticket from an origin station on one system to Grand Central. It is valid on both peak and off-peak trains.[85][86]

Today's LIRR signal system has evolved from its legacy Pennsylvania Railroad (PRR)-based system, and the railroad utilizes a variety of wayside railroad signals including position light, color light and dwarf signals.[111] In addition, much of the LIRR is equipped with a bi-directional Pulse code cab signaling called automatic speed control (ASC), though portions of the railway still retain single direction, wayside-only signaling. Unlike other railroads, which began using color-light signals in the 20th century, the LIRR did not begin using signals with color lights on its above ground sections until 2006.

Some portions of the railway lack automatic signals and cab signals completely, instead train and track car movements are governed only by timetable and verbal/written train orders, although these areas are gradually receiving modern signals.[112] Many other signals and switching systems on the LIRR are being modernized and upgraded as part of the Main Line's Third Track Project, most notably at Mineola, where the system is being completely redone and modernized.[113]

A Long Island Rail Road M9, showing the dual-type contact shoe.

On portions of the railroad equipped with ASC, Engineers consult the speed display unit, which is capable of displaying 7 speed indications. As a result of a December 1, 2013, train derailment in the Bronx on the Metro-North Railroad, railroads with similar cab signal systems to Metro-North, such as the LIRR, were ordered to modify the systems to enforce certain speed limit changes, which has resulted in lower average speeds and actual speed limits across the LIRR.[114]

The LIRR's electrified lines are powered via a third rail at 750 volts DC with the contact shoe running along the top of the rail, similar to on the New York City Subway and PATH systems.[115] This system is incompatible with Metro-North's third rail, which is under-running, though the M8 and M9 fleets are capable of using both types of third rails, as they are equipped with both types of contact shoes.

The LIRR's electric fleet consists of 836 M7 and 170 M3 electric multiple unit cars in married pairs, meaning each car needs the other one to operate, with each car containing its own engineer's cab. The trainsets typically range from 6 to 12 cars long.

In September 2013, MTA announced that the LIRR would procure new M9 railcars from Kawasaki.[116] A 2014 MTA forecast indicated that the LIRR would need 416 M9 railcars; 180 to replace the outdated M3 railcars and an additional 236 railcars for the additional passengers expected once the East Side Access project is complete.[117] The first M9s entered revenue service on September 11, 2019.[118]

C3 Bi-level coaches at grade crossing in Bethpage

The LIRR also uses 134 C3 bilevel coaches powered by 24 DE30AC diesel-electric locomotives and 20 DM30AC dual-mode locomotives. They are used mostly on non-electrified branches, including the Port Jefferson, Oyster Bay, Montauk, Central, and Greenport Branches. There are also 23 MP15AC locomotives in use as work trains and yard switchers.[119]

• Cannonball, a Friday-only 12-car train to Montauk running May through October, with two all-reserved parlor cars with full bar service. Since May 24, 2013, it has originated at Penn Station with a Sunday evening return from Montauk; only the westward train stops at Jamaica. The two rear cars ("Hamptons Reserve Service") have reserved seating and exclusive bar service.[120] The name is a nod to the Cannon Ball, the all-year train to Montauk from the 1890s until the 1970s. It carried parlor cars and standard-fare coaches and ran weekday afternoons from Long Island City, then from Penn Station until 1951, when DD1 operation, and changing engines at Jamaica, ceased.[121]

• Fisherman's Special (1932–1950s) from Long Island City to Canoe Place Station and Montauk via Jamaica, April through October, terminating at Canoe Place in April, extended to Montauk in May. Served Long Island fishing trade.[122]
• Peconic Bay Express / Shinnecock Bay Express (1926–1950) from Long Island City to Greenport and Montauk, Saturday only, express to Greenport and Montauk. Discontinued during World War II though revived for a few seasons afterwards.[121]
• Shelter Island Express (1901–1903, 1923–1942) from Long Island City to Greenport, Friday-only summer express that connected to Shelter Island ferries.
• Sunrise Special (1922–1942) ran during the summer, NY Penn to Montauk on Fridays and westbound Mondays. In summer 1926 it ran daily. All parlor car (no coaches) from 1932 to 1937.[105][106][123][124][125]

The freight-only Bay Ridge Branch through Brooklyn

Some non-electrified lines are used only for freight:

• The Garden City-Mitchel Field Secondary is a short remnant of the Central Branch that splits from the Hempstead Branch at Garden City, running to Uniondale near Hofstra University and Nassau Veterans Memorial Coliseum. This branch does not host any NYAR service. This branch was used by the Ringling Bros. Circus to transport animals, staff and equipment to the Nassau Coliseum until their final shows there in May 2017.[48]
• The Bushwick Branch runs west from the Montauk Branch at Maspeth to Bushwick Terminal. This was a passenger branch until 1924.[131]^: 128
• The Bay Ridge Branch runs south and west from the Montauk Branch at Fresh Pond to Bay Ridge. At Fresh Pond, it meets CSX's Fremont Secondary, which goes over the Hell Gate Bridge towards Upstate New York and New England. At its southern end it interchanges with the New York New Jersey Rail, LLC cross harbor rail barge service to New Jersey. This branch had a passenger service until 1924.[132] The entire line was electrified with overhead wire in 1927,[133] and the overhead wires were dismantled in 1969.[131]^: 10

The East Side Access project built a LIRR spur to Grand Central Terminal that will run in part via the lower level of the existing 63rd Street Tunnel.[134] The East Side Access project added a new eight-track terminal called Grand Central Madison underneath the existing Grand Central Terminal.[134] The project was first proposed in the 1968 Program for Action, but due to various funding shortfalls, construction did not start until 2007.[135] As of April 2018, the project was expected to cost $11.1 billion and was tentatively scheduled to start service in December 2022.[136][137] It opened on January 25, 2023, with limited shuttle service between Jamaica and Grand Central.[138] Full service to Grand Central began on February 27, 2023.[139]

Several "readiness projects" were also completed to increase peak-hour capacity across the LIRR system in preparation for expanded peak-hour service after the completion of East Side Access.[140][141][142] The LIRR constructed a new platform for Atlantic Terminal-bound trains at Jamaica station,[143] converting most Atlantic Branch service between these two stations into a high-frequency shuttle.[24] The LIRR also installed a new storage track east of Massapequa and extended one east of Great Neck station,[142][144] in addition to expanding the train yard at Ronkonkoma.[142][145][146] An expansion of the yard at Port Washington was also proposed, but as of September 2022, the MTA has not come to an agreement with the Town of North Hempstead,[147]^: 65 resulting in the project being postponed indefinitely.[148][149]^: 61

There are also plans to build a new station in the Queens neighborhood of Sunnyside, in between the New York terminals and the Woodside station, serving as a rail hub for all LIRR branches and potentially some Amtrak and New Jersey Transit trains, as well.[150] The Sunnyside station is to be built after the completion of East Side Access, due to current capacity constraints.[150]

• 
  One of Grand Central Madison's lower level platforms under construction in January 2019
• 
  The new pocket track in Massapequa, located in between the two outer tracks, as viewed from a passing Babylon Branch train
• 
  Construction on Jamaica's new platform in August 2019

The completed second track, as viewed from the reconstructed Wyandanch station.

In 2012, the LIRR started adding a second track along the formerly single-tracked section of the Main Line between Farmingdale and Ronkonkoma stations to increase track capacity and allow for enhanced service options.[151] The project was completed in September 2018.[152][153]

As part of the preparations for East Side Access's opening,[154] the LIRR also widened the two-track sections of the Main Line between Floral Park and Hicksville stations to three tracks, in addition to eliminating each of the grade crossings and rebuilding all of the stations along this stretch of the Main Line.[155][156] Work on the third-track project started in September 2018.[157][158] The project was completed in 2022, in time for the opening of East Side Access.[159][160]

The larger Belmont Park Redevelopment Project called for a new Elmont station between the Queens Village and Bellerose stations on the Main Line, to better serve the new UBS Arena in the Nassau County neighborhood of Elmont.[161] It is the first new station built by the LIRR in nearly 50 years; the last new station added was the former Southampton College station on the Montauk Branch, which opened in 1976 and closed in 1998, due to low ridership and the high cost of installing high-level platforms for the then-new C3 railcars.[162] The eastbound platform of the Elmont station officially opened in November 2021,[163] while the westbound platform opened in October 2022.[164]

As part of the MTA's 2020–2024 Capital Program, the Central Branch, shown here, will be electrified.

As part of the 2020–2024 MTA Capital Program, the Central Branch of the LIRR will be electrified, to allow for enhanced service options and capacity, and to mitigate service disruptions, should one arise.[34]

There have also been many pushes by residents and politicians over the past several decades – most recently by New York Senator Jim Gaughran – to electrify the remainder of the Port Jefferson Branch between the Huntington and Port Jefferson stations, in addition to the remainder of the Oyster Bay Branch between the East Williston and Oyster Bay stations to enhance service in the served areas and to upgrade service capacities along the lines; electrifying these lines could lead to more frequent direct service to and from Manhattan, as diesel trains are not allowed in Penn Station and dual-mode trains exceed the clearance for the 63rd Street Tunnel into Grand Central Madison.[165][166][167]

The LIRR has a long history of tense relations with its passengers.[169] Daily commuters have long had complaints about the LIRR's service. According to a 1999 article in The New York Times, the LIRR's service woes were long considered part of the "unholy trinity of life on Long Island," along with the Long Island Lighting Company's high rates and the Long Island Expressway's traffic snarls.[170] Various commuter advocacy groups have been formed to try to represent those interests, in addition to the state mandated LIRR Commuters Council.[171]

The LIRR has been criticized for not providing additional service to the East End of Long Island as the twin forks continue to grow in popularity as a year-round tourist and residential destination. Demand is evidenced by flourishing for-profit bus services such as the Hampton Jitney and the Hampton Luxury Liner and the early formative stages of a new East End Transportation Authority.[172] Local politicians have joined the public outcry for the LIRR to either improve the frequency of east end services, or turn the operation over to a local transportation authority.

Critics claim that the on-time performance (OTP) calculated by the LIRR is manipulated to be artificially high. Because the LIRR does not release any raw timing data nor does it have independent (non-MTA) audits it is impossible to verify this claim, or the accuracy of the current On Time Performance measurement. The percentage measure is used by many other US passenger railroads but the criticism over accuracy is specific to the LIRR. As defined by the LIRR, a train is "on time" if it arrives at a station within 5 minutes and 59 seconds of the scheduled time.[173] The criterion was 4 minutes and 59 seconds until the LIRR changed it because of a bug in their computer systems.[174]

Critics[175] believe the OTP measure does not reflect what commuters experience on a daily basis. The LIRR publishes the current OTP in a monthly booklet called TrainTalk.[176] TrainTalk was previously known as "Keeping Track."[177] A more accurate way to measure delays and OTP has been proposed.[178] Called the "Passenger Hours Delayed" index it can measure total person-hours of a specific delay. This would be useful in comparing performance of specific days or incidents, day-to-day (or week-to-week) periods, but has not been adopted.

Ridership has increased from 81 million passengers in 2011 to 89.3 million passengers in 2016, which is the railroad's highest ridership since 1949. The all-time highest ridership was in 1929, when 119 million passengers rode 1.89 billion passenger miles.[179] This increase in ridership has been attributed to the increased usage of the LIRR by millennials, and the increase of reverse-peak travel.[180]

A New York Times investigation in 2008 showed that 25% of LIRR employees who had retired since 2000 filed for disability payments from the federal Railroad Retirement Board and 97% of them were approved to receive disability pension. The total collected was more than $250,000,000 over eight years.[181] As a result, Railroad Retirement agents from Chicago inspected the Long Island office of the Railroad Retirement Board on September 23, 2008. New York Governor David Paterson issued a statement calling for Congress to conduct a full review of the board's mission and daily activities. Officials at the board's headquarters responded to the investigation stating that all occupational disability annuities were issued in accordance with applicable laws.[181]

On November 17, 2008, a former LIRR pension manager was arrested and charged with official misconduct for performing outside work without permission. However, these charges were all dismissed for "no merit" by Supreme Court Judge Kase on December 11, 2009, on the grounds that the prosecution had misled the grand jury in the indictment.[182]

A report produced in September 2009 by the Government Accountability Office stated that the rate at which retirees were rewarded disability claims was above the norm for the industry in general and indicated "troubling" practices that may indicate fraud, such as the use of a very small group of physicians in making diagnoses.[183]

Another series of arrests on October 27, 2011, included two doctors and a former union official.[184][185]

According to court documents, from 1998 through 2011, 79% of LIRR retirees obtained federal disability when they retired. On August 6, 2013, a doctor and two consultants were found guilty in connection with the accusations and sentenced to prison.[186][187][188]

In 2018, LIRR foreman Raymond Murphy was discovered at or near his home on 10 separate occasions whilst claiming overtime pay. Murphy earned $405,021 in 2017, of which $295,490 was overtime. According to reports, he was allowed to retire with a full public pension before being reprimanded or punished.[189]

In 2021, LIRR employee and track inspector Thomas Caputo and co-conspirators John Nugent and Joseph Balestra were federally convicted for large-scale overtime fraud.[190] Caputo was paid approximately $461,000 in 2018, of which $344,000 was supposed overtime. He claimed to have worked 3,864 overtime hours, an average of more than 10 hours of overtime for all 365 days the year. Phone, bank, email, and other records revealed many of these hours were fraudulent: Caputo was clocked in during vacation and while attending outside social events such as a bowling league.