The following outlines the History of the Staten Island Railway from 1971 to the present. The Staten Island Railway's (SIR) Tottenville line, a rapid transit line in the New York City borough of Staten Island, was turned over to the Staten Island Rapid Transit Operating Authority (a division of New York state's Metropolitan Transportation Authority) on July 1, 1971, and the line was purchased by the city of New York. Freight on the line would continue to be handled by the B&O under the Staten Island Railroad. The MTA ordered new trains and renovated stations in the 1970s and 1980s. SIRT was transferred from the New York City Transit Authority's Surface Transit Division to its Department of Rapid Transit in 1993. MetroCard fare payment was introduced in 1994, and fares were removed from most of the line in 1997. A short section of the easternmost portion of the mostly-abandoned North Shore Branch was reopened for passenger service to the Richmond County Bank Ballpark between 2001 and 2010. Further changes in the 21st century included accessibility improvements; the construction of a new Arthur Kill station in the 2010s; and new trains and OMNY fare payment in the 2020s.

Meanwhile, freight service (part of the North Shore Branch), formerly part of the Baltimore and Ohio Railroad (B&O), became part of the larger Chessie System in a merger with the Chesapeake and Ohio Railway (C&O), and the island's freight operation was renamed the Staten Island Railroad Corporation in 1971. Only a few isolated industries on Staten Island continued to use rail services, and in 1985, the Chessie System sold its Staten Island Railway branch to the New York, Susquehanna and Western Railway (NYS&W), a Delaware Otsego (DO) subsidiary. The NYS&W subsequently retained the Staten Island's freight operations; in 1989, the NYS&W ended all freight service to Saint George. In 1991, the Arthur Kill Bridge was removed from service, and the line's final freight train operated in1992. The North Shore Branch and the Arthur Kill Bridge were then taken over by Chessie's successor, CSX Transportation (CSX). 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. During the early 2000s, the Port Authority of New York and New Jersey announced plans to reopen the Staten Island Railroad line in New Jersey. SThe freight line connection from New Jersey to the Staten Island Railroad was completed, and became operated in part by the Morristown and Erie Railway in 2006.

City operation of passenger service: 1971–present

Transfer to MTA operation: 1968–1971

In May 1968, the President of the Metropolitan Transportation Authority (MTA), William Ronan, proposed that New York City take control of the SIRT and spend $25 million on modernizing the line. This proposal was part of a 20-year, $2.9-billion plan announced by the agency on February 28. Some of the money allocated to the SIRT would be used to purchase new trains. On December 18, 1969, the Board of Estimate approved the purchase of the SIRT for $1 and the use of $3.5 million to purchase the line's 48 cars, of real estate, the air rights over the tracks, and the line's Clifton Shops. The additional land was purchased to allow for a wider right-of-way, parking lots, and station improvements. As part of the agreement, the Baltimore & Ohio Railroad (B&O) would continue to operate freight service over the line once a day.

On January 1, 1970, New York City's lease of the Tottenville line was terminated; after that date the city reimbursed the railroad for its passenger deficits. On May 29, 1970, New York City and the SIRT entered an agreement for NYC to purchase the Tottenville line, as part of which the SIRT was reserved the right to operate freight service over the line. The city was required to ensure the track was in good condition for SIRT's freight operations. The freight operation was reorganized as the Staten Island Railroad Corporation. On June 29, 1970, the Staten Island Rapid Transit Operating Authority was incorporated as a subsidiary of the state's MTA to acquire and operate the SIRT.

On April 21, 1971, the ICC approved the city's purchase of the line. On July 1, 1971, operation of the Tottenville line was turned over to the Staten Island Rapid Transit Operating Authority, a division of the state's MTA. The line itself was purchased by the City of New York for $1 and the MTA paid the B&O $3.5 million for the line's equipment. Grade crossings along the Tottenville line had to be removed by the B&O to finalize the deal. Grade crossings were supposed to have been eliminated in the 1930s but a lack of finances—partially resulting from the Great Depression and World War II—prevented it.

Despite MTA improvements, problems persist: 1970s and 1980s

On June 15, 1972, five 1955-built, air-conditioned coaches on loan from the Long Island Rail Road (LIRR) went into service on the SIRT. One three-car train made one round trip during the morning and operated again during the afternoon peak. As a result of previous tests, the edges of the platforms at St. George were trimmed for the extra clearance required by the LIRR cars, which were long. The cars were only longer than the 45 cars in operation but had a seating capacity of 123 passengers—almost double the capacity of the other coaches.

On February 1, 1972, the fare on the SIRT was increased for the first time since 1958, to 35 cents from an average fare of 22 cents; the system used to have zoned fares. The fare increase applied to the whole system and was accompanied by the elimination of commutation tickets and student tickets. Previously, fares ranged from 20 to 35 cents. Sixteen percent of riders of the 17,000 daily riders had no change in fare. There was a 10 percent increase for 51 percent of passengers and a 15 percent increase for the remaining 33 percent. The fare increase was expected to bring in an extra $400,000 a year.

At the time, the line was operating at a deficit of $2.9 million a year, with $2.5 million of it offset by a subsidy from the city. The MTA had plans for a $25 million improvement program for the line including new train cars. Improvements were also planned for the tower and signal systems, for the roadbed and for the stations. Increased power, of new rails, and mercury-vapor lighting at 14 of the 22 stations were also part of the plan. Three quarters of the $25 million were to be provided by 1967 state transportation bond issue and the remaining $6.25 million was to be paid by the city.

On February 28, 1973, the first six new R44 cars were put into service on the SIRT. These were part of a 52-car order from the Saint Louis Car Company—the same type of cars as the newest cars then in use on subway lines in the other boroughs. The R44s replaced the ME-1 rolling stock inherited from the B&O that had remained in continuous service since 1925 when the system was electrified.

During the 1970s, the MTA's ability to improve service on the line was hampered by several strikes by the SIRT's workers. From December 11, 1975, to April 1976, service on the SIRT was shut down because the line's 61 motormen and conductors went on strike. The strike ended once the MTA agreed to give them 14% wage increases.

In December 1976, SIRTOA recently completed projects to provide remote control of SIRT's electrical substations from the central one at St. George, and to install a two-way radio system. The former project improved the reliability of the system's power system, while the latter provided direct communication between the St. George control center and all trains, allowing information about the status of SIRT operations to be sent immediately to train staff and passengers on trains.

In December 1977, SIRTOA was preparing to begin construction on a pair of projects that would allow longer four-car trains to be run during rush hours regularly. New York City covered 25 percent of the cost of the projects, while New York State covered the remaining 75 percent. The first project was the construction of a new electrical substation capable of handling 4,000 kilowatts in Grant City, and the second was the expansion and modernization of the repair shop at Clifton Yard.*

Work on the new Grant City substation building, which would cost $506,592, was expected to start in January 1978 and be completed by March 1979, while the installation of electrical equipment, which would cost $1.8 million, would begin in September 1978 and be completed in 1980. The project was the first in a series of improvement part of a long-term program to upgrade the SIRT's electrical supply and make it more reliable. In later phases, the new equipment installed in the new Grant City substation would also be installed in older substations on the line. In response to complaints from nearby residents, the design of the substation was modified to blend in with the character of the surrounding residential area, and would be constructed within the SIRT's open cut right-of-way. In addition, greenery and shrubs would be installed to beautify the structure's roof, which was located at street level. Work on the project was finally underway in April 1979, and was expected to be completed by the end of 1980.

The Clifton Yard project was planned to improve the maintenance of the SIRT's new fleet of R44 cars. This $3.9 million project, as of December 1977, was expected to begin in 1978 and be completed by the end of 1979. The project would extend and modernize the car maintenance shop, and construct new storage facilities, and a new two-story motor and wheel repair shop. The extension of the existing maintenance shop would allow the inspection pits to be rebuilt. These pits were designed to fit the ME-1 cars, which were shorter than the R44 cars. The improvements at the shop would increase the number of cars that could be overhauled and inspected daily by 50 percent. As of April 1979, work was expected to be completed by the middle of 1980.

On August 6, 1980, an MTA committee evaluated whether it should continue operating the rail line. On September 28, 1981, Assemblyman Robert Straniere announced that half of the $25 million allocated for capital improvements to the SIRT from bond use funds would be used for improved power distribution and the modernization of stations. Eleven stations would have their platforms extended, completing the extension of platforms along the line and two stations would have their wooden platforms replaced. In addition, equipment at four substations would be improved, new switches would be installed at Tottenville interlocking, and the wye track at St. George would be realigned to fit four-car trains, among other improvements. As part of the MTA's inaugural Capital Program from 1981, Pleasant Plains and Prince's Bay stations were rebuilt and the platforms at several other stations were lengthened.

On September 23, 1985, SIRTOA began work to repair structural problems at ten stations, including crumbling stairways. Temporary access paths, platforms and stairways were constructed to allow service to be maintained while work was underway.

On October 22, 1986, midday service was reduced in frequency from one train every 20 minutes to one every 30 minutes, due to a reduction in ferry service. Weekend service was reduced by 15 trains to 78 and weekday service was reduced by 15 to 109. In the following two years, ridership reduced from 6.47 million to 6.23 million.

Improvements in fare collection: 1985–1994