The Port Jefferson Branch is a rail line and service owned and operated by the Long Island Rail Road in the U.S. state of New York. The branch splits from the Main Line just east of Hicksville and runs northeast and east to Port Jefferson. Several stations on the Main Line west of Hicksville are served primarily by trains bound to/from the Port Jefferson branch, so LIRR maps and schedules for the public include that part of the Main Line in the "Port Jefferson Branch" service.

The Port Jefferson Branch is the busiest branch of the LIRR, with frequent electric service to Huntington where electrification ends, and diesel service east of Huntington continuing to Port Jefferson. The MTA also refers to the line as the "Huntington/Port Jefferson Branch" or "Huntington Branch".

Service Port Jefferson Branch service (as distinct from the physical trackage called the Port Jefferson Branch) extends east from Floral Park, where the Hempstead Branch separates from the Main Line. The line west of Huntington is electrified and double tracked. 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. East of there, the line is single-track, with a double-ended freight siding at Greenlawn, an interlocked passing siding east of Northport, and further interlocked sidings at Kings Park, Smithtown and Stony Brook passenger stations, allowing trains traveling in opposite directions to pass each other.

Electric trains on the branch operate between Manhattan (Penn Station or Grand Central) and Huntington, providing local service on the branch. Trains to the Ronkonkoma Branch provide supplemental service; these usually run express, stopping only at Mineola and/or Hicksville. Additional service to Mineola is provided by Oyster Bay Branch trains, and a handful of Montauk Branch trains also stop at Mineola and Hicksville on weekdays, though the vast majority of Montauk Branch trains that run on the Main Line do not stop. Service on the non-electrified portion of the branch between Port Jefferson and Huntington is usually provided by diesel shuttles; transfers generally occur at Huntington between diesel shuttles and electric trains to/from city terminals. During rush hours, the branch sees extra service, including direct service between stations east of Huntington and Hunterspoint Avenue, Long Island City, or Penn Station.

Stations on the electrified portion that have the heaviest traffic include Mineola (Main Line), Hicksville (Main Line), and Huntington. On the non-electrified portion, the heaviest traffic tends to be to the Stony Brook station where Stony Brook University is located.

History The line from Hicksville to Syosset was chartered in 1853 as the Hicksville and Syosset Railroad and opened in 1854. The LIRR later planned to extend to Cold Spring Harbor, but Oliver Charlick, the LIRR's president, disagreed over the station's location, so Charlick abandoned the grade and relocated the extension south of Cold Spring, refusing to add a station stop near Cold Spring for years. Another argument at Huntington led to the line bypassing the town two miles (3 km) to the south, though a station was built. The line was extended from Syosset past Huntington to Northport in 1868, , June 2004 Edition and in 1873 the 1870-chartered Smithtown and Port Jefferson Railroad opened from a mile south of Northport to Port Jefferson, , February 2005 Edition turning the old line into the Northport Branch, the result of another argument between Charlick and Northport. The extension required the construction of the Kings Park and Smithtown Trestles.

The Port Jefferson Branch was extended to Wading River in 1895, and became known as the Wading River Branch. The line was once slated to continue eastward and rejoin the Main Line at either Riverhead or Calverton. From 1905 to 1928, Wading River was also the site of a LIRR demonstration farm. The other one was east of Medford station on the Main Line.

The grade crossing with New York Avenue in Huntington was eliminated in 1909 as that road was lowered below grade. In 1910 and 1911 work was undertaken to reduce grades and eliminate sharp curves along the line between Syosset and Huntington. The project eliminated grade crossings, shortened the line by , and provided two million yards of excavated material that could be used for the reconstruction of Jamaica station. In 1911, the line's second track was extended from Hicksville to Cold Spring. In 1985, the second track was extended from just east of Syosset to just west of Huntington to alleviate a single-track bottleneck.

The line east of Port Jefferson was abandoned in 1938. The right-of-way is now owned by the Long Island Power Authority and used for power lines. A parallel rail trail for bicycling, running, and walking opened in 2022. The Port Jefferson Branch was electrified from Mineola to Huntington in 1970. The former Northport Branch was abandoned in 1985, and the Kings Park Psychiatric Center spur (see below) was abandoned in 1988.

Kings Park Psychiatric Center Spur

The Kings Park Psychiatric run-off (KPPC) is an abandoned spur off the Port Jefferson Branch for the Kings Park Psychiatric Center. 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.

This spur was first used in 1896 for coal and passenger use on Sundays. The route was the second-largest spur in the Long Island Rail Road system when it was first completed. The route came to an end during the late 1980s.Mileposts 43-44 Kings Park (Bob Emery Map; September 1957; TrainsAreFun.com) Nowadays, this abandoned route is a right-of-way for biking and is open to the public today. Only small fragments of rail remain, as it most of it was removed during the demise of the complex.Kings Park State Hospital Spur (Train Web)

Electrification On October 19, 1970, electrification was extended from Mineola to Huntington, the eastern limit of electrification on the branch. This was the first major LIRR electrification project since the electrification of the Babylon Branch in 1925 between Lynbrook and Babylon. The project was completed for $69 million, and received funding from a 1967 state transportation bond issue and the United States Department of Transportation. 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.

Since then, the LIRR has aspired to extend electrification beyond Huntington, however, it has not yet been done so. Due to this, stops Huntington and west see three times as much service than east.

In the 1980s, the railroad prepared to extend electrification to at least Northport, or Smithtown, although electrification of the Ronkonkoma Branch on the Main Line was seen as a higher priority, in part because the Main Line's central location in Suffolk County would benefit a larger number of people.

In December 1983, the LIRR announced that it was taking steps in the electrification of the branch, with the first step being the addition of a second electrified track from Syosset to Huntington. The second built along the south side of the existing track. The second track was expected to be open in 1986. In August 1983, Long Island Lighting Company started relocating its power line along the right-of-way between these points. The following month a contract to prepare the site and to construct the roadbed for the track was awarded for $9.5 million. 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. As part of the project, the south platform was to be extended to accommodate 12-car trains. The design of the project to Northport was completed, and preliminary designs were expected to be completed by early 1984.

On August 6, 1984, a groundbreaking ceremony was held at Kings Park station for the inauguration of a project to install high-level platforms at that station in preparation of the electrification of the line from Huntington to Smithtown. Kings Park would receive high-level platforms first, with Greenlawn, Northport, and Smithtown also slated to receive them. Work was to be completed in two phases. In the first phase, expected to be completed by the end of 1984, six-car high-level platforms would be installed. These platforms would be extended to accommodate twelve-car trains in the second phase, to be done by the middle of 1985.

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. Financial constraints acted as another obstacle to electrification to Northport. McIver also did not want to electrify the branch in a piecemeal fashion and wanted to wait until the railroad had the funds to electrify from Huntington to Port Jefferson all at once. 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. Because electrification has not occurred, these 12-car platforms are unique in the LIRR's diesel territory; the high-level platforms along the Montauk, Greenport and Oyster Bay diesel branches are all much shorter. Work to install centralized traffic control between Smithtown and Port Jefferson started in fall 1974 and was completed in March 1975. This project was intended to improve safety and to increase train speed. The change allowed bidirectional service in single-track territory with the use of passing sidings.

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 second track sped some trips by up to 15 minutes, and increased operational flexibility. The $41 million project started in September 1983 and included the widening of bridges at West Rogues Path and Woodbury Road, five rubberized grade crossings, and the installation of a six-car length platform on the new second track at Cold Spring Harbor. Construction for the project required off-peak service outages starting in June 1985, and its completion was delayed from fall 1985 due to delays in property acquisition in Cold Spring Harbor.

Instead of electrification, the LIRR ultimately pursued dual-mode locomotives that could switch between diesel power and electric power to serve Penn Station (where diesel emissions are banned). Senator Norman Levy said that "The people who ride the line would have just about all the positive aspects of electrification with this proposal." 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.

Proposed electrification extension In 2015, multiple parties renewed calls for electrification of the branch. The LIRR estimated that electrification would cost up to $18 million per track mile, so electrification of the 23 miles from Huntington to Port Jefferson could cost approximately $414 million. In its 20-Year Needs Assessment, the agency lists electrification eastward as a long-term goal.

In September 2018, LIRR President Phillip Eng said the LIRR is still exploring the possibility of electrifying the remaining section of track between Huntington and Port Jefferson.