The 63rd Street Tunnel lay unused for over a decade, and its lower level, intended for future Long Island Rail Road (LIRR) service, was completed solely to support the subway line above it.

[9][10] Beneath the subway tunnel is a lower level used by the Long Island Rail Road (LIRR), where it heads to Grand Central Madison.

[22] On October 17, 1963, the Board of Estimate approved a new East River tunnel sited at 64th Street, noting that it would cost $30 million and take seven years to build.

[25] The Board of Estimate approved the revised 63rd Street route on January 14, 1965, at a budget of $28.1 million and a four-year timetable, with the connections to the rest of the transit network awaiting a study that was then scheduled for completion in mid-1966.

[29] In November 1967, voters approved a $2.5 billion transportation bond issue, and in early 1968, under the Program for Action, officials provided detailed plans for how it would be used.

[32] Groundbreaking ceremonies for the line took place on November 24, 1969, at Vernon Boulevard and 21st Street in Queensbridge Park, Long Island City.

Four 38-foot-square (12 m) prefabricated sections of the 63rd Street Tunnel were constructed at Port Deposit, Maryland, then towed to New York and sunk under the East River.

[41] The next month, Mayor John Lindsay told city engineers to write a report that studied ways to reduce the project's impact.

[40] The results of the report, released in January 1971, called for using tunnel boring machines underneath Central Park to reduce disruption.

[43] Later that month, the NYCTA finally agreed to halve the width of the proposed 75-foot (23 m)-wide cut, which resulted in a proportionate decrease in the area of affected parkland.

[2] In May, construction was briefly halted when residents jumped into utility pits to protest the cutting of trees near the Lexington Avenue station.

[52] In summer 1976, the NYCTA announced that "it will take an extra five or six years—until 1987 or 1988—to complete the new Manhattan–Queens trunk subway line from Central Park to Jamaica via the new 63rd Street tunnel."

As an interim measure, the NYCTA proposed a new station at Northern Boulevard, adjacent to Queens Plaza, which could possibly open by 1983 or 1984.

They have advanced equipment – welded tracks, fluorescent lighting and rubber-based pads under the rail – that have not yet been installed on most of the system's 230 operating miles.

This year, the contractor will tear down his two-story office in Central Park, remove the fence near Fifth Avenue and restore foliage and the bird house he damaged, at a cost of $300,000.

By 1981, five years after completion of the tunnel, the Transit Authority expects to put it to use; its brand new quiet tracks will be used as a storage yard for out-of-service trains.

It was a temporary wall, erected by the NYCTA in 1971 to block unauthorized entry into the site of the 63rd Street Line running underneath the Central Park Zoo.

[57] Armored with polished aluminium in the futile hope of resisting spray-paint and permanent marker ink, the wall did little to dissuade teenage graffiti writers from climbing over and descending into the tunnel during its construction.

[57] The name came about because the Central Park Zoo at that time was a classical 19th-century menagerie, populated by wild animals displayed in open-air cages, who paced the bars back and forth neurotically—always hoping for an escape, yet paradoxically blind to the world beyond their cramped quarters.

ALI noted that by contrast, here were these feral teenagers, himself included, living in a free society, who sought nothing more wholeheartedly than to crowd together in a deep, dark hole in the ground.

The article now noted that the Queens super-express had been deferred "to 1988 at the earliest", and the only sections in progress were the 63rd Street Line to Northern Boulevard, and "a small piece along Archer Avenue".

Richard Ravitch, the MTA chairman, said that to stop the work was "so costly as to make it impractical subsequent to the construction of the subway portion."

[62] The MTA was studying four options for making this line more useful:[60][63][61] The suburban Glendale, Ridgewood and Middle Village communities in central Queens strongly opposed any proposals involving the Montauk Branch, which ran through their neighborhood.

[64][65] The ultimately agreed-on plan was to connect the tunnel to the local tracks of the IND Queens Boulevard Line, at a cost of $222 million, and a timetable of at least eight years.

[73] In August 1985, at the instigation of Senator Al D'Amato, the federal government suspended funding on both the 63rd Street and Archer Avenue projects over "concerns with the construction management practices".

[78] From May to November 1995, the north side of the Manhattan Bridge was closed for reconstruction during middays and weekends and the Q train was routed via Broadway at this time.

[80] The 1998–1999 reconstructions were to replace the tracks, which had become deteriorated after eight years of use due to a flaw in the railway ties; namely, an "innovative" design of "shallow epoxy-and-sand pads" had weakened the base of the rails.

The construction project also extended the lower level LIRR tunnel and involved a number of other elements, including the integration of ventilation plants, lowering a sewer siphon 50 feet, rehabilitation of elements of the existing line, mitigating ground water, diverting trains which continued to run through the project area and widening of the entry point to the Queens Boulevard Line to six tracks.

[95] As part of a $107 million project,[96]: 123  the tunnels were scheduled to experience numerous service disruptions in 2023 to accommodate replacement of direct fixation track and cables, installation of new signal equipment, leak remediation, and repairs to concrete surfaces.

An F shuttle train would run between Lexington Avenue-63rd Street and 21st Street-Queensbridge, stopping at Roosevelt Island, at all times except late nights.