From Pennsylvania Station (MP 0.0), New York City, the southward NEC departs past the crossovers at A Tower (MP 0.2), where the Empire Connection departs on the south side, and plunges into the double track Hudson [North] River Tunnel (speed limits 60-20), passing into New Jersey at MP 1.2, and passing the Weehawken Shaft at MP 1.8, emerging from the Hudson River tunnel and crossing the New Jersey meadowlands (speeds now 90/75-50), passing above the former Conrail and the Susquehanna north-south line and turning southwest, past crossovers at Bergen (MP 3.7), with passenger speeds rising to 90 mph at the W44-W45 signal bridge,, crossing above the former Conrail Croxton yard, and the relocated former Erie Bergen County Line and former Lackawanna Main Line at the location of the NJT Secaucus Transfer interchange station (MP 4.9). This station has platforms serving four tracks on each of the two levels; there are two outer platforms and a center island on the NEC at Secaucus Transfer, with the center island serving two reversible center tracks. Interchange is at the level above all of the tracks, requiring all interchanging passenger to go up before they can go down to the other set of platforms. Two additional tracks were added on the south side of the original formation on the NEC for the span of the station.
The NEC line then crosses above the former New York & Greenwood Lake line, past crossovers at Portal (MP 6.0), over the movable bridge across the Hackensack River (speeds 70-10 across the bridge), past the site of a closed former Erie line and the crossovers at Swift (MP 7.2) for the connectors at the Kearney Connection, where the NEC interconnects with the former Lackawanna line passing below it, with connectors on both the north and south sides of the NEC for the use of NJT trains. The most easterly crossover at Swift is from track 2 (eastbound) to track 3 (westbound), which is followed by the connector from track 3 to the north side of the Morris & Essex line passing more than 50 ft. below. There is then a crossover from westbound track 3 to eastbound track 2, followed by the switch where the eastbound connector heads off to connect with the M&E below. Both connectors join the north side of the M&E line, with crossovers allowing access to any of the three tracks on that line.
This line is electrified with overhead AC catenary, double track, heavy with commuter trains.