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 begins at the Main Line just east of Hicksville station, and runs northeast and east to Port Jefferson. LIRR maps and schedules indicate that the Port Jefferson Branch service continues west along the Main Line to Floral Park, which is where the Hempstead Branch begins to parallel the Main Line. However, the Hempstead Branch does not merge with the Main Line until east of Queens Village, and so the Main Line between Floral Park and Queens Village is served by Hempstead Branch trains.
Port Jefferson Branch service in Nassau County begins when the Hempstead Branch separates from the Main Line at the Queens Interlocking in Bellerose. The line from Queens Interlocking to Huntington is electrified and double tracked. Electrification extends to a point east of Huntington before Greenlawn Station on a layup track for electric trains. The line east of that point is not electrified and has a single track with passing sidings at Greenlawn, east of East Northport, Kings Park, Smithtown and Stony Brook.
Stations on the electrified portion that have the heaviest traffic include Mineola, Hicksville, and Huntington. On the non-electrified portion, the heaviest traffic tends to be to the Stony Brook station where the State University of New York at Stony Brook is located.
There are occasional plans to electrify this line past Huntington, at least to Northport, in conjunction with the construction of a planned new electric train yard, to alleviate overcrowding and service limitations on the Ronkonkoma Branch, and to otherwise accommodate increased ridership expected once the East Side Access project to Grand Central Terminal is completed. As of 2006, funding for this project has been deferred to a future capital budget and preparation of the Environmental Impact Statement has been suspended.
In addition, a third Main Line track from Bellerose to Mineola has also been proposed in order to provide increased services.
Most Port Jefferson electric trains operate the full route from Penn Station to Huntington. Supplemental service is provided on Ronkonkoma Branch trains to Mineola and Hicksville. Additional service to Mineola is provided by Oyster Bay Branch trains, and some Patchogue-bound Montauk Branch trains also stop at Mineola and Hicksville during the weekdays. Also, one Montauk-bound train makes a stop at Hicksville overnight on weeknights. During off-peak hours, including weekends, a diesel shuttle runs between either Hicksville or Huntington and Port Jefferson. During rush hours, there are specialized services to and from stations west of, and including, Huntington Station. These services provide for express service, through service to Flatbush Avenue, and service to Penn Station that bypasses Jamaica. Also, east-of-Huntington service is extended to Jamaica, Hunterspoint Avenue, Long Island City, or Penn Station.
The line from Hicksville to Syosset 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, and in 1873 the Smithtown and Port Jefferson Railroad opened from a mile south of Northport to Port Jefferson, turning the old line into Northport into the Northport Branch, the result of another argument between Charlick and Northport.
The Port Jefferson Branch formerly extended to Wading River in 1895, and 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 an LIRR Demonstration farm. The other one was east of Medford Station on the Main Line. 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 but there are plans to create a rail trail for bicycling, running, and walking. The Port Jefferson Branch was electrified to Huntington Station in 1970. The former Northport Branch was abandoned in 1985, and the Kings Park Psychiatric Center spur was abandoned in 1988.
On a small note electrification reached from Mineola to Hicksville & Huntington in 1970. For 15 years from Amott Interlocking east of Syosset Station to west of Huntington it was single-tracked. In 1985, they constructed a second electrified track in that area to avoid the single track bottle neck, this included Cold Spring Harbor adding a second platform.
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The Port Jefferson Branch has also been known to have the most hazardous grade crossings in the country. In 1982 a van was struck by a diesel train at the Herricks Road crossing in between Mineola and Merillon Avenue. The crossing for many years was dubbed by the NTSB as "The most dangerous crossing in the U.S." In 1998 after a complicated project the crossing was finally eliminated with the tracks now going over a bridge. Ten years later Roslyn Road also in Mineola was eliminated in the same fashion. Other hazardous crossings along the branch west of Huntington are Robbins Lane & Jackson Avenue in Syosset, School Street in Westbury, Willis Avenue in Mineola, and New Hyde Park Road, 12th Street, and Covert Avenue in New Hyde Park.