The Port Jefferson Branch is a LIRR branch that leaves the Main Line just after Hicksville and is electrified for its first 10 miles to Huntington with the remaining 23 miles out to Port Jefferson still diesel territory. Off-peak service on the line is generally from hourly or better (every half-hour on weekends) electric trains that run from Penn Station to Huntington, where connecting diesel ‘scoot’ shuttle trains run every 90 minutes the remaining distance to Port Jefferson. A few midday diesel trains are extended to Hicksville for connections to Ronkonkoma branch trains at certain times to keep the 90 minute off-peak diesel train frequency, when there is only hourly electric train service to/from Huntington. The Port Jefferson Branch timetable is also the timetable for all intermediate stops on the Main Line between New Hyde Park and Hicksville that are primarily served by Huntington trains with the Main Line (Ronkonkoma Branch) trains skipping these stations. The timetable shows all trains that stop at Mineola and Hicksville, which means nearly all Ronkonkoma Branch trains and Oyster Bay Branch trains are also on the Port Jefferson branch timetable since most trains make these two important intermediate stops (Mineola and Hicksville are listed on these timetables with NOTE, telling passengers to consult a Port Jefferson branch timetable for all train service for these stops).

During rush hours service on the line increases, service to Port Jefferson is provided by through diesel trains to and from Jamaica. Two of these trains provide one-seat rides into Penn Station using dual-mode locomotives, and 4 additional Port Jefferson round-trips run to Hunterspoint Avenue (with most continuing to Long Island City). This is in addition to electric service between Huntington and Atlantic Terminal Brooklyn (including one PM peak express train that runs non-stop from Atlantic Terminal skipping Jamaica to its first stop at Westbury).

The double-tracked nature of the Main Line (which requires throating during the peak of rush hours when both tracks are used for trains operating in the same direction) means there are gaps in reverse-peak service with no trains arriving in Huntington between 6:52 and 8:54 (both of these trains continue to Port Jefferson), and no trains leaving Huntington between 5:11pm and 6:29pm (with no trains leaving Port Jefferson between 4:06pm and 8:34pm, although there is a 6:49pm inbound scoot train that originates at Stony Brook).

The branch off the Main Line was originally fully dieselized and single tracked with passing sidings. In one of the Long Island Rail Road’s first electrification expansion projects under public ownership from the MTA under a Federal Grant electric service was extended from Mineola (where it arrived in 1910), reaching Huntington in 1970. In December 1983 the LIRR announced it was planning to fully electrify the branch, which included a new electrified second track opening on the line between Huntington and Syosset on June 9, 1986, making electric territory fully double-tracked as exists to this day. In anticipation of the extension of electrification full 12 car long high-level platforms were built at all stations on the branch out to Port Jefferson by 1986, making these stations unique in diesel territory compared to the much shorter platforms built for C3 diesel trains in the late 1990s. At first the LIRR considered extending electrification only to Northport but management at the time decided to wait until they had the funding to electrify the rest of the branch.

This electrification never happened with the funds set aside instead used for the building of West Side Yard in 1987. To improve service the LIRR decided instead to pursue a different path by purchasing new dual mode locomotives they claimed could provide all the benefits of electrification of a one-seat ride into Penn Station – although only for a few rush hour trips – without the major costs involved with electrification. The LIRR first did this by purchasing 10 prototype multi-level C1 cars and rebuilding 3 FL9 locomotives from Metro-North. Dual-mode service into Penn Station began in August 1991 and was a success. The LIRR placed a full order for 130 new C3 multi-level cars and 46 new DE30AC and DM30AC that were all delivered between 1997 and 1999. This finally gave customers in diesel territory new train cars, replacing the previous diesel P72/PT75 series coaches that dated to the 1950s (although 130 new multi-level cars were purchased to replace 233 passenger cars, meaning the LIRR has a lack of diesel territory equipment that continues to this day, which is particularly evident by the crowds on Summer Weekends when the comfort of regular commuters are sometimes sacrificed to run more and longer trains on the Montuak Branch).

The other downside to the fact electrification was never extended beyond Huntington is that Huntington, although an important transfer point and terminus lacks, the features that would make operations more efficient. The stop has no train yard, just a couple of storage tracks for 2 to 3 trains to layup, this means long deadheads (some trains deadhead as far away as the West Side Yard) to provide electric passenger service. In addition, the station just has two side platforms, this means passengers changing between electric and diesel trains must get off their train, wait for all passengers to be discharged, wait for the terminating train to leave before their new train enters the station just behind it. Cross-platform transfers are generally faster and more efficient, since the new connecting train can leave before the terminating train and passengers don’t have to wait on the platform for all connecting passengers to get off. Ideally this branch would be fully electrified to Port Jefferson, which also includes a decently sized train yard and would smooth operations and provide one-seat ride all day service for the entire branch. Instead it seems the LIRR will just keep expanding parking lots on the electrified Ronkonkoma branch that is 5 to 10 miles to the south or at Huntington which are driven to my many commuters even if there is a closer stop to their home on the diesel portion of the Port Jefferson branch with its much inferior train service.