Conrail's Northern Branch runs from their Passaic and Harsimus Line at Marion Junction in western Jersey City, New Jersey, (via a short connection known as the Marion Running Track) north to a junction with CSX's Bergen Subdivision and Northern Branch at CP 2 in North Bergen, New Jersey.
Recently, the line was improved to handle traffic that had formerly used Conrail's River Line on the east side of the New Jersey Palisades, which is now used for the Hudson-Bergen Light Rail. New Jersey Transit paid for the project, which included double-tracking the line, changing Marion Junction and Bergen Junction, and building overpasses on Secaucus Road and Paterson Plank Road.
Because of these recent changes, the Northern Branch now serves as part of a major CSX rail corridor from Upstate New York to the rest of the country. CSX's Northern Branch (which was owned by Conrail until the 1998 split) continues north to the New York state line, and is a minor spur. Through traffic moves onto the Bergen Subdivision (formerly Conrail's River Line) at CP 2.
North of there, the line passes under the old Delaware, Lackawanna and Western Railroad and its Boonton Branch, now owned by New Jersey Transit, in the middle of West End Junction. These bridges were built in 1908 or 1909, before which the tracks crossed at grade.
Just north of the NJ Transit overpasses, the line enters Bergen Junction, and two tracks split to the west. The western one again splits in two; one of the tracks merges with New Jersey Transit's Bergen County Line, and the other passes under the first and heads west under the old DL&W Boonton Branch, merging with what had been New Jersey Transit's Boonton Line until 2002, when the Montclair Connection opened.
The other track that splits north of the Boonton Branch underpass proceeds up a grade and over a bridge, merging back into the main line after the bridge. Under this bridge is another track splitting west from the main line, which heads northwest to Norfolk Southern Railway's Croxton Yard. Before this split, the line coming through the Erie Railroad's old tunnel (now the Nave-Croxton Running Track, leading to the National Docks Secondary) merges with the line. Until the recent rebuilding, the overpass was the only way to continue north; trains from the south not using it were forced onto the track to Croxton, while trains from the north were forced onto the National Docks.
Soon the line passes over County Road on a rather old bridge. It then passes under Secaucus Road, whose bridge opened on May 20, 2002. The New York, Susquehanna and Western Railway begins at the Land Bridge Terminal, just north of Secaucus Road, and parallels the Northern Running Track, just to the west, all the way to its end.
The Northern Branch ends at North Bergen Yard, at what has been called Granton Junction, and is now CP 2. From here, it splits into two CSX lines, the Bergen Subdivision (which was part of Conrail's River Line until most of Conrail's assets were split), and the Northern Branch, which ends at the New York state line, and was also a Conrail line until recently. The Bergen Subdivision soon becomes the River Subdivision, and leads along the west side of the Hudson River towards Albany, New York.