The western segment between Hicksville and Ronkonkoma sees 24-hour service to Penn Station and Grand Central Madison in New York City.

The eastern segment between Ronkonkoma and Greenport is served by diesel-electric trains, and only sees a handful of trips each day.

The eastern segment is also the only dark territory area of the Long Island Rail Road, meaning that it does not have signals.

[5] The western segment of the line from Hicksville to Ronkonkoma was electrified in 1987,[6] creating a one-seat ride to Penn Station.

Formerly, service on this segment was provided by diesel trains, which could not enter Penn Station, requiring a transfer.

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 2012, the Metropolitan Transportation Authority (MTA) started adding a second track to the line between Farmingdale and Ronkonkoma to increase capacity.

The LIRR is required to install a positive train control signaling system on all its trackage by the end of 2018.

[5] The MTA initially budgeted $29 million in its 2015–2019 capital program to add signals along the 10 mile segment from Ronkonkoma to Yaphank.

[15][16] However, in a 2017 amendment[17] of the capital program, the agency postponed the construction of the new signal system, only including $2 million to fund design.

[25] This phase also involved rehabilitating grade crossings, demolishing pedestrian bridges, and building a second platform Wyandanch.

This will allow the LIRR to provide additional service in diesel territory, thereby saving travel time.

[31]: 64–65 In 2015, the MTA conducted environmental studies to determine the impact of expanding the existing rail yard in Ronkonkoma.

[32] 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 Deer Park option was dismissed as it would have impacted several grade crossings, duplicated employee facilities and as it would not have benefited riders east of the station.

[26]: 88, 204 To accommodate a projected increase in Long Island Rail Road ridership following completion of the East Side Access project to Grand Central Terminal, and to expand local and reverse-peak service, a third track was built on the Main Line between Floral Park and Hicksville.

This short segment would eventually become the eastern end of the Third Track, and already allowed for a slight increase in peak-hour service upon its completion.

[49][50][51][52] In January 2016, Governor Andrew Cuomo announced a transportation improvement plan which included several million dollars in funding to restart third track development.

"[57] In December 2017, the LIRR awarded a contract for the project to the consortium 3rd Track Constructors for $1.8 billion, with construction beginning in 2018 and completion estimated for 2022.