Penn Station's passenger facilities are located at the floors immediately below ground level, in the block bounded by 31st Street, 7th Avenue, 33rd Street and 8th Avenue. Below these facilities, well underground, are the tracks and platforms, accessed from the concourse level by a mezzanine level and two pedestrian bridges, each with stairways and escalators to or from the platforms. There are 21 total passenger tracks, numbered consecutively from south to north, with Tracks 1 to 16 accessible from the main Amtrak/New Jersey Transit concourse, Tracks 1 to 12 accessible from a separate NJ Transit East End Concourse, and Tracks 13 to 21 accessible from the separate Long Island Railroad concourses to the east of the main concourse, and from teh concrouse west of Eighth Avenue. Tracks 18 to 21 are used exclusively by the LIRR.
At the track level, there are four west-facing stub-end tracks on the south side (Tracks 1 to 4), served by the two southernmost platforms, and used exclusively by NJT. North of these are nine island platforms, serving tracks five to twenty-one (one track has two platform faces, one on either side), with the tracks grouped in the eastern throat such that Tracks 5 to 17 can access the more southerly eastward tunnel, and tracks fourteen to twenty-one can access the more northerly eastward tunnel. In the westerly throat, all tracks can access the westerly tunnel to New Jersey, and all have access to storage tracks on the west side either north (including the LIRR West Side Yard, located west of 10th Avenue) or south of that tunnel. Only a limited number of tracks (5 to 8) can access the west-side connection. Tracks 5 to 21 have both AC and DC electrification: AC is 11.3 kV, 25 Hz, overhead catenary; DC is 600-750 V, third-rail.
From Pennsylvania Station (MP 0.0), New York City, the southward NEC departs past the crossovers at A Tower (MP 0.2), in the short open air section west of the Farley Post Office Building (on the west side of 8th Avenue), 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 a road bridge overhead, just west of the tunnel portal, a deck girder bridge over the former Conrail and the Susquehanna north-south line and turning southwest at Allied (MP 4.1), past signals at MP W3.4, crossovers at Bergen (MP 3.7), a bridge over a street, Intermediate Signals, passenger speeds rising to 90 mph at the MP W4.4-W4.5 signal bridge, a bridge over a street, a deck girder bridge 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 passengers 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 passes a through girder bridge over the meadows, signals at MP W5.5, a highway alongside to the north, a through girder bridge over the former New York & Greenwood Lake line, signal bridges and crossovers at Portal (MP 6.0), the through truss movable bridge across the Hackensack River (speeds 70-10 across the bridge), the site of a closed former Erie line, a bridge over an angled street, and the signal bridges and 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 sides of the NEC descending to the north side of the former Lackawanna 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 Lackawanna 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. After the voltage change from the NEC's 11.3 kV, 25Hz to NJT's 25kV, 60Hz, 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.