Electrification extends east of Huntington, past a layup track used to store electric trains, to a point between the Park Avenue and Lake Road grade crossings.

Trains to the Ronkonkoma Branch provide supplemental service; these usually run express, stopping only at Mineola and/or Hicksville.

The project eliminated grade crossings, shortened the line by 3,300 feet (1.0 km), and provided two million yards of excavated material that could be used for the reconstruction of Jamaica station.

This spur started just west of Kings Park station, ran north of the station house, crossed Indian Head Road (Suffolk CR 14) and then curved north to cross New York State Route 25A, where it ran along the western edge of the hospital property, and ended at the Hospital's coal power plant.

With the completion of electrification to Huntington, six trains would run from electric territory on the branch in the morning, and five would return in the evening, providing direct service to Brooklyn and Penn Station without a change at Jamaica.

In December 1983, grading and construction work was expected to begin that month, and track installation was scheduled to be completed by the end of 1985.

[17] Bruce McIver, president of the LIRR at the time, estimated in 1986 that electrification of the branch would cost $320 million, including new rolling stock.

He argued that the limited funds the railroad had set aside for electrification would be better spent on other improvements, such as signal and yard upgrades near Penn Station.

In anticipation of electrification, from late 1985 to early 1986, the LIRR built full-length high-level platforms at all stations between Huntington and Port Jefferson.

Work to install centralized traffic control between Smithtown and Port Jefferson started in fall 1974 and was completed in March 1975.

[19] On June 9, 1986, double-tracking of the line between Syosset and Huntington was completed, and seven additional trains (two diesels and five electric) were added to the schedule.

The $41 million project started in September 1983 and included the widening of bridges at West Rogues Path and Woodbury Road,[21] five rubberized grade crossings, and the installation of a six-car length platform on the new second track at Cold Spring Harbor.

"[24] The LIRR's dual-mode locomotives debuted in the late 1990s, providing two round trips during weekday rush hours between Penn Station and Port Jefferson, the first time a one-seat ride was available.

[31][32] On April 28, 1998, a bridge over Herricks Road opened, replacing a grade crossing which was once "labeled the most hazardous in the United States by the National Transportation Safety Board."

Several hazardous crossings still exist west of Huntington east of DIVIDE interlocking, such as Robbins Lane and Jackson Avenue in Syosset.

The Third Track project closed the seven remaining grade crossings on the Main Line, namely those in Westbury, Mineola, and New Hyde Park.

After construction of retaining walls, pedestrian walkway, and the repaving of the road, Urban Avenue was officially reopened on September 5, 2019.

From May 2020 to November 2020, School Street underwent a grade crossing elimination and reopened less than two years after a violent accident occurred involving a pick-up truck and two trains.

As a result, electric trains must deadhead to Huntington for rush hour service from as far away as West Side Yard in Manhattan, about 37 miles (60 km) away.

In the early 2000s, the MTA performed environmental studies for over a dozen potential sites for a yard between Huntington and Smithtown.

One commenter asserted that a yard would turn the communities along the line into the MTA's "storage closet" for East Side Access.

Other opponents of the plan argued that the MTA should extend electrification to Port Jefferson and use its existing diesel rail yard.

[37][38] The MTA budgeted $8 million in its 2015–2019 Capital Program for environmental studies, design work, and land acquisition for a new electric yard.

)[39][40] As of 2019[update], the MTA was also considering other options, including extending electrification and/or a second track from Huntington to Port Jefferson.

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.

[54][55][56][57] In January 2016, Governor Andrew Cuomo announced a transportation improvement plan which included several million dollars in funding to restart third track development.

"[62] 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.

[72][73] West of New Hyde Park, trips go on to terminate at Penn Station, Hunterspoint Avenue, Grand Central, or Jamaica.