Ronkonkoma Branch

Electrified portion

The western segment of the line from Hicksville to Ronkonkoma was electrified in 1987, eliminating diesel service between Ronkonkoma and Hicksville and creating a one-seat ride to Penn Station. Average rush-hour trip time from Ronkonkoma to Penn Station decreased from 97 minutes pre-electrification (including the mandatory transfer from a diesel to an electric train) to 71 minutes afterwards. The $168.5 million project attracted many new passengers: A survey of peak-hour Ronkonkoma Branch passengers conducted by the LIRR in April 1988 found that 42 percent of the branch's passengers were new to the line: 34 percent switched from other lines (the Port Jefferson and Montauk Branches), 6 percent were new to the LIRR as a whole and 2 percent recently returned to the LIRR. By September 1988, over 2,000 new riders during the morning rush hour had switched to the Ronkonkoma branch, much of which occurred in the first month after electrification, faster than the LIRR expected. Commuters complained that the expanded parking facilities at Ronkonkoma built in anticipation of electrification were overcrowded and already inadequate, and that double-parking and vandalism were rampant. In the decades since, the amount of parking at Ronkonkoma has expanded. In the present, diesel locomotives continue to provide all service between Ronkonkoma and Greenport. As electrification occurred in the 1980s, the MTA also planned to double-track the line between Farmingdale and Ronkonkoma, however, this was deferred due to lack of funds.

Greenport Branch

The 46 miles between Ronkonkoma and Greenport is one of the few dark territory areas on the Long Island Rail Road that does not have signals. The relatively small amount of train movements on this segment are governed by train orders and timetable authority. This segment is served by diesel-electric "scoots", all but one of which terminate at Ronkonkoma, requiring customers traveling west of Ronkonkoma to transfer there. Two eastbound and three westbound scoots travel each weekday between Ronkonkoma and Greenport. Also, one eastbound and two westbound trains each weekday run between Ronkonkoma and Riverhead, and one eastbound each weekday runs as far as Yaphank. In addition, one eastbound train, nicknamed the "Jury Duty Special", runs between Deer Park and Riverhead in the morning, intended for use by Suffolk County jurors. This train is unique among the scoots in that it has no connection from Nassau County and New York City; only passengers in Suffolk County can access this train. This is because capacity constraints on the Main Line preclude eastbound reverse-peak service. The "Jury Duty Special" is also the only scoot that serves stations west of Ronkonkoma. The Greenport Branch has seasonal weekend service from early May to late November, consisting of two round-trips each day between Ronkonkoma and Greenport. On Fridays during the summer, the eastbound trip to Yaphank is extended to Greenport, and one evening trip runs from Greenport to Jamaica, running express between Ronkonkoma and Jamaica. Added in summer 2016, this is the only Greenport scoot trip to serve the New York City terminals.

The LIRR has tried to discontinue service east of Ronkonkoma on several occasions, citing minimal service due to low ridership. In 2010, the idea was entertained by the financially troubled MTA, who proposed eliminating all scoot service except for the popular summer weekend service. Ultimately, weekday service remained, but weekend service outside of the summer (defined as Memorial Day-Columbus Day) was discontinued. In 2013, the span of weekend service was extended to operate from early May to late November. On July 25, 2016, the LIRR announced that year-long weekend service between Ronkonkoma and Greenport would be restored in 2016.

Despite proposing to eliminate most service east of Ronkonkoma, the MTA desires to enhance the segment's infrastructure. The MTA budgeted $29 million in 2015 to add signals along the 10 mile segment from Ronkonkoma to Yaphank. This upgrade will install signals, track circuits and automatic speed control (ASC). In its 20-Year Capital Needs Assessment, the MTA describes extending electrification eastward from Ronkonkoma to Yaphank or Riverhead, as well as the addition of a second-track between Ronkonkoma and Yaphank as long-term needs. However, the MTA cites the high cost of electrification and other components as a barrier to present-day action. If electrification were to be extended eastward, stations would also need upgrading as all station platforms east of Ronkonkoma are only long enough to fit one train car.

Central Branch

Some LIRR maps also include as part of the Ronkonkoma Branch the non-electrified Central Branch, which splits from the Ronkonkoma Branch east of Bethpage and connects with the more southern Montauk Branch, just west of Babylon. There are no stations along this stretch, and it is mainly used by trains with diesel-electric engines going express from Jamaica to Babylon. No trains using this track appear on Ronkonkoma Branch schedules; they appear on Montauk Branch and Babylon Branch schedules, and some appear on schedules for Mineola and Hicksville on the Main Line, if a stop is scheduled there.

Second track between Farmingdale and Ronkonkoma

In 2012, the MTA approved a project to build a second track between Ronkonkoma and Farmingdale, a well anticipated event since the electrification of the rail line in the 1980s. Currently, the only areas east of Farmingdale with two tracks are between Deer Park and Brentwood stations (including those stations), at Central Islip station, and finally at Ronkonkoma itself. This construction will take place on land already owned by the LIRR (acquired during the 1980s electrification of this segment) so no land acquisition is required. It will include upgrades to switches, grade crossings, and station facilities. The project will be done in two phases:

The project officially got underway in August 2015. With the help of a New Track Construction machine, workers officially laid the second track between Ronkonkoma and Central Islip within a year, with some work still to be done. There were a few weekends with no service, and in addition, a few grade crossings were closed for two days to add the second track to the crossings. A design–build contract for phase 2 was awarded in June 2016. In August 2016, workers started to clear brush and make space for Phase 2 east of Deer Park near Wyandanch.

The benefits of the project include increased operational flexibility, increased reverse-peak service between Farmingdale and Ronkonkoma, and increased off-peak service between Hicksville and Ronkonkoma—operating half-hourly instead of just hourly—as well as increased resilience for the system, as this additional capacity will allow the Main Line to better serve as a substitute for South Shore lines in case of a disturbance caused by extreme weather.

Mid-Suffolk Yard

In 2015, the MTA conducted environmental studies to expand the existing rail yard in Ronkonkoma. This expansion, called the Mid-Suffolk Yard, will add 11 new tracks, increasing the number of total tracks from 12 at present to 23. The expansion will use space already owned by the MTA located immediately to the south of the existing rail yard and north of MacArthur Airport. The increase in storage space will allow the MTA to increase peak-hour service once East Side Access is complete and service to Grand Central begins. The project is budgeted for $76.6 million, and the MTA expects to finish construction by late 2018. Other locations along the line considered for a new electric yard but rejected include Deer Park, Central Islip, and Yaphank. Reasons given include the cost of land acquisition, the fact that the Deer Park option would impact several grade crossings, duplicate employee facilities and would not benefit customers east of Deer Park, the fact that the proposed Central Islip site (Connetquot River State Park) is State parkland, and the high cost of electrification and station upgrades between Ronkonkoma and Yaphank.

Possible reopening of Republic Station

The MTA has expressed interest in reopening Republic station, located between Farmingdale and Pinelawn, which closed in 1987 as part of electrification between Hicksville and Ronkonkoma. At the time, the station only had about a dozen riders daily, which didn't make it very cost-effective to upgrade the station to support electric railcars.

However, within the last decade, there has been an increased amount of commercial and residential development along Route 110 near the station, which has led to the MTA looking into re-opening Republic station.

The reopened station would serve the Route 110 corridor, a major north-south commercial route. The station was deferred from the MTA's 2010-2014 budget due to budgetary issues, but revived in 2012. The MTA budgeted $5 million in 2015 to design a new station and carry out environmental studies, although construction itself has not been funded yet. The rebuilt station will have two new 12-car platforms, and ADA-compliant ramps.

Signalling between Ronkonkoma and Yaphank

The 46 miles between Ronkonkoma and Greenport is one of the few dark territory areas on the Long Island Rail Road that does not have signals. The MTA budgeted $29 million in 2015 to add signals along the 10-mile segment from Ronkonkoma to Yaphank. This upgrade will install signals, track circuits, and automatic speed control (ASC).