Two tracks from the Paoli direction, with an extra track to their west, and two tracks from the North Philadelphia direction, running on the south side of Zoo Tower and north of the Amtrak tracks from 30th Street's lower level, come together at the south end of the Zoo Interlocking. The SEPTA double-track line departs from the Amtrak line on the west side of the line south of Zoo Interlocking (MP 1.9), with many other tracks in the vee of the junction, some becoming the Hi-Line freight tracks, and others becoming yard tracks remaining at the lower level. The SEPTA tracks climb up southward and turn east, past the junction with the tracks from Phil at West (MP 1.1), below the former high-line bridge, with many other tracks in the vee of the junction at West, some proceeding at upper levels, above the tunnel to University, into the upper level of Philadelphia 30th Street station (MP 0.9).
At Phil, there is a Tower on the south side of the NEC, with a bridge from the Hi-Line that descends on the south side. From Phil/Arsenal (MP 2.3), on the west side of the Schuylkill, the SEPTA double-track line climbs up northward, past a bridge over a street below, University City (MP 1.7), which has a center island platform with umbrella shed, and a station up above, and Walnut (MP 1.4), where there is a tunnel, and turns east, in tunnel, past the junction with the tracks from Zoo, at West (MP 1.1), below the former high-line bridge, into the upper level of Philadelphia 30th Street station (MP 0.9).
The upper level of 30th Street station has three double-sided platforms serving six through tracks. (Tracks 3 & 4 are on the northernmost platform, serving trains headed westbound at the station; tracks 5 & 6 are on the center platform, with track 6 serving westbound trains and track 5 serving eastbound trains, and tracks 1 & 2 are on the southernmost platform, serving trains headed eastbound at the station. Each track serves trains headed for specific routes.)
East of the station, within which these tracks bridge over the Northeast Corridor tracks below, the tracks bridge over the Schuylkill Expressway, below, pass crossovers at Schuylkill (MP 0.8), where the number of tracks reduces from six to four, cross the Schuylkill River into Center City Philadelphia, above a street and then the CSX line on the east bank of the river, past two bridges over streets, crossovers at 20th Street (MP 0.6), the mouth of the tunnel that becomes the Center City Tunnel, and crossovers at Broad (MP 0.4), through Suburban Station (MP 0.0, two platforms serving four tracks, with extra tracks and extra platforms on both sides, from the PRR days), where there is an isolation changeover between the former PRR and former Reading electrification systems, and directly into the City Center Tunnel, past crossovers at Juniper (MP 0.2), and crossovers at Mark (MP 0.4), among the four tracks in the tunnel, through the Market East underground station (MP 0.5, two platforms serving four tracks), just east of the location, above, of the stub end of the former Reading Terminal, turning north past crossovers at Vine (MP 0.8) and emerging from the tunnel in the vicinity of the former Spring Garden Street station on the line out of the erstwhile Reading Terminal, passing a signal bridge just north of the tunnel mouth, and climbing up onto the viaduct, still extant, in parts, west of the climb, that used to carry the lines out of that station, bridging over six streets, past a closed factory on the west side, crossovers and signal bridges at Brown (MP 1.6/1.1), the former location of the Green Street servicing facility on the west side of the line, and the station at Temple University (MP 2.1), which has two high-level island platforms with umbrella sheds.
Rundown row houses line the streets just to the north of the Temple University football field on the west side. The line then curves north-northwest, with several extra tracks on the east side, past six bridges over streets, two road bridges overhead, a pedestrian bridge overhead, a road bridge overhead, and the station at North Broad Street (MP 2.9), with low-level platforms on the outer tracks only, and under the four through girder bridges carrying the Northeast Corridor lines, just to the east of that line's North Philadelphia station, a former track connection into a building on the east side descending and trailing in, crossovers, a road bridge overhead, a line descending on the west side, and the junction at 16th Street Junction (MP 3.5), where the double track line northwest to Norristown splits away, on the west side, from the four track main line.