thumb|Bond of the New Jersey Junction Railroad Company, issued 30. June 1886
left|thumb|A 1921 map of the New Jersey Junction Railroad.
The New Jersey Junction Railroad (NJJ) was part of the New York Central Railroad and ran along the Hudson River in Hudson County, New Jersey, from the West Shore Railroad (NYCRR) yards at Weehawken Terminal south to Jersey City. It later owned an extension to the north, separated by the Weehawken yard from the original line.
What would become part of the NJJ was the Hoboken and Hudson River Turnpike, chartered in 1857 to build a road from the north of Hoboken to Bull's Ferry near the Bergen County line. The New York and Bull's Ferry Railroad was chartered in 1861, and renamed the New York and Fort Lee Railroad the year after. The first two miles of this projected road, built on part of the Hoboken and Hudson River Railroad from Jersey City to the north side of Hoboken, opened in 1870, and was controlled by the Erie from the outset. The connection to the Long Dock Tunnel was made by way of the Morris and Essex Railroad; when they abandoned their line in favour of using the Bergen Tunnels, the Fort Lee assumed control of the connection to the tunnel. By the end of its life, the road reached the Township of Union.
With the opening of the Weehawken Tunnel by the NYCRR in 1884, the NYCRR began to expand their reach through Hudson County. The NJJ was incorporated under the laws of New Jersey on February 27, 1886. The New York and Fort Lee was leased to the New Jersey Junction Railroad on June 30, 1886. On July 1, 1886, the NJJ was leased for 100 years to the New York Central and Hudson River Railroad. The full line south to the Pennsylvania Railroad's lines in Jersey City opened for freight in May 1887 and passengers in June 1887.