[14]: 1255 By 1880 the railway was barely operational, and New York State sued (through Attorney General Hamilton Ward) to dissolve the company in May of that year.

[16]: 4 [17]: 8 Construction of the Vanderbilt's Landing-to-Tompkinsville portion of the North Shore Branch began on March 17, 1884,[10]: 230 [12]: 37 [18] and the line opened for passenger service on August 1 of that year.

[26] In 1889, construction began on the Baltimore and New York Railway— 5.25-mile (8.45 km) line from Arthur Kill to the Jersey Central at Cranford, and was finished later in the year.

[35] During the 1920s, a branch line along Staten Island's West Shore was built to haul building materials for the Outerbridge Crossing.

The Gulf Oil Corporation opened a dock and tank farm along Arthur Kill in 1928; to serve it, the Travis Branch was built south from Arlington Yard into the marshes of the island's western shore to Gulfport in the early 1930s.

[37] Freight and World War II traffic helped pay some of the SIRT's accumulated debt, and the line was briefly profitable in the 1940s.

The need to transport war materiel, POW trains and troops made the stretch of the Baltimore & New York Railway between Cranford Junction and Arthur Kill extremely busy.

[9]: 8  The new bridge could rise 135 feet (41 m) and, since it aided navigation on Arthur Kill, the federal government assumed 90% of the project's $11 million cost.

[12]: 173 Only a few isolated industries on Staten Island continued to use rail services, and the yard at Saint George was essentially abandoned.

[60] The NYS&W subsequently retained the Staten Island's freight operations, which served only ten customers by that time, and they had hopes of attracting more to boost profitability on the line.

[60] In 1989, the NYS&W embargoed the trackage east of Elm Park on the North Shore Branch, ending all freight service to Saint George.

The line and bridge were sold again in 1994 to the New York City Economic Development Corporation (NYCEDC), followed by a decade of false starts.

[67] No turnstiles were installed at the other stations on the line, and passengers at St. George began paying when entering and exiting;[68] fares had previously been collected on board by the conductor.

[75]: 102–103 The Staten Island Railway uses Baltimore & Ohio Railroad-style color position light signals dating back to its B&O days.

As part of the project, forty R44 subway cars and four locomotives were modified with onboard cab signaling equipment for ATC bi-directional movement.

[98] Before the 1997 introduction of the one-fare zone,[99] with the MetroCard's free transfers from the SIR to the subway system and MTA buses, fares were collected from passengers boarding at stops other than St. George by onboard conductors.

[100] In the past, passengers had avoided paying the fare by exiting at Tompkinsville and walking a short distance to the St. George Ferry Terminal.

So all New England and southern freight could pass through the New York metropolitan area, two rail tunnels from Brooklyn (one to Staten Island and the other to Greenville, New Jersey) were planned.

[104] On December 15, 2004, a $72 million project to reactivate freight service on Staten Island and repair the Arthur Kill Vertical Lift Bridge was announced by the NYCEDC and the PANYNJ.

[105] In 2006, the freight line connection reopened from New Jersey to the Staten Island Railroad, including the Arthur Kill Bridge.

[106] Regular service began on April 2, 2007 (16 years after it had closed)[107] to ship container freight from the Howland Hook Marine Terminal and other industrial businesses.

[111] As of 2019, the New York City Department of Sanitation's contractor was moving containers of municipal solid waste by barge from Queens and Manhattan to the Howland Hook Marine Terminal for transfer to rail there.

Elected officials on Staten Island, including State Senator Diane Savino, have demanded the replacement of the railway's aging R44 cars.

[127] Although the Metropolitan Transportation Authority initially planned to order R179s for the Staten Island Railway, it was later decided to overhaul R46s to replace the R44s.

[127]: 17–18 Several proposals have been made to connect the SIR to the subway system, including the abandoned, unfinished Staten Island Tunnel and a line along the Verrazzano-Narrows Bridge using B Division cars and loading gauge, but economic, political and engineering difficulties have prevented these projects from realization.

[133][134] In a 2006 report, the Staten Island Advance explored the restoration of passenger service on 5.1 miles (8.2 km) of the North Shore Branch between St. George and Arlington.

[8][50][51] A small portion of the western end is used for freight service as part of the ExpressRail intermodal network at the Howland Hook Marine Terminal.

[111][149] The North Shore Branch served Procter & Gamble,[104] United States Gypsum,[150] shipbuilders and a car float at Saint George Yard.

Although the right-of-way has been redeveloped, most of it is still traceable on maps; Lily Pond Avenue is built over the right of way where it passes under the Staten Island Expressway.

The spur, built in 1928, was called the West Shore Line by the B&O Railroad and delivered building materials to the Outerbridge Crossing construction site near Arthur Kill.