The LIRR is one of two commuter rail systems owned by the MTA, the other being the Metro-North Railroad in the northern suburbs of the New York area.

[10] As of 2018[update], the LIRR's budget for expenditures was $1.6 billion plus $450 million for debt service, which it supports through the collection of fares (which cover 43% of total expenses) along with dedicated taxes and other MTA revenue.

In 1900, the Pennsylvania Railroad (PRR) bought a controlling interest as part of its plan for direct access to Manhattan which began on September 8, 1910.

[7] 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.

[20] As of April 2018[update], the project was expected to cost $11.1 billion and was tentatively scheduled to start service in December 2022.

[27][31][32] An expansion of the yard at Port Washington was also proposed, but as of September 2022[update], the MTA has not come to an agreement with the Town of North Hempstead,[33]: 65  resulting in the project being postponed indefinitely.

The City Terminal Zone includes portions of the Main Line, Atlantic, and Montauk Branches, as well as the Amtrak-owned East River Tunnels to Penn Station.

Additionally, the Long Island Rail Road operated trains over portions of the Brooklyn Rapid Transit (BRT) elevated and subway lines until 1917.

[66] In addition to its daily commuter patronage, the LIRR also offers the following services: 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.

[93] 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.

[101] As part of a one-year pilot program starting in July 2024, monthly tickets for LIRR trips entirely within New York City would also receive a 10% discount.

[105]: 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.

[108] 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.

This new ticket would provide the same discounts as a regular CityTicket, while also having protections against fare evasion, given the unique nature of the Far Rockaway Branch's route.

[114][115] 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.

[116] In 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 LIRR is one of the last railroads in the United States to use mechanical interlocking control towers to regulate rail traffic.

At additional locations, line side towers control the various switches and signals in accordance with the timetable and under the direction of the Movement Bureau in Jamaica.

[133] For most of its history LIRR has served commuters, but it had many named trains, some with all-first class seating, parlor cars, and full bar service.

[140] Both areas are primarily served by trucking for freight haulage, an irony in a region with the most extensive rail transit service in the Americas, as well as the worst traffic conditions.

[142] In May 1997, freight service was franchised on a 20-year term to the New York and Atlantic Railway (NYAR), a short line railroad owned by the Anacostia and Pacific Company.

On the western end it provides service on the surviving freight-only tracks of the LIRR: the Bay Ridge and Bushwick branches; the "Lower Montauk" between Jamaica and Long Island City; and to an interchange connection at Fresh Pond Junction in Queens with the CSX, Canadian Pacific, and Providence and Worcester railroads.

[65] There have also been many pushes by residents and politicians over the past several decades – most recently by former New York State 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, 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 height clearance for the 63rd Street Tunnel into Grand Central Madison.

[154] 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.

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.

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.

[169][170][171] In 2018, LIRR foreman Raymond Murphy was discovered at or near his home on 10 separate occasions whilst claiming overtime pay.

[172] 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.

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.