In-depth planning for a dedicated transport system at JFK began in 1990 but was ultimately cut back from a direct rail link to an intra-borough people mover.

[12] Another proposal, made by the Port Authority of New York and New Jersey in 1987, called for a rail line to connect all of JFK Airport's terminals with a new $500 million transportation center.

[14][15] In 1978, the MTA started operating the JFK Express, a premium-fare New York City Subway service that connected Midtown Manhattan to the Howard Beach–JFK Airport station.

[11] The Port Authority, foreseeing economic growth for the New York City area and increased air traffic at JFK, began planning for a direct rail link from the airport to Manhattan.

[24] In 1990, the MTA proposed a $1.6 billion rail link to LaGuardia and JFK airports, which would be funded jointly by federal, state, and city government agencies.

[29] The EIS, conducted by the New York State Department of Transportation and the Federal Aviation Administration (FAA), found the plan to be feasible, though the project attracted opposition from area residents and advocacy groups.

The Port Authority had suggested the heavily trafficked corner of Lexington Avenue and 59th Street,[25][27][29] though many nearby residents opposed the Manhattan terminal outright.

As a result, the Port Authority considered abridging the rail link plan, seeking federal and state funding, partnering with private investors, or terminating the line at a Queens subway station.

[33] The New York Times wrote that 21 prior recommendations for direct rail links to New York-area airports had been canceled in the preceding 30 years,[33][43] while the Engineering News-Record said 22 such proposals had failed.

[43][49] Giuliani wanted the Port Authority to study extending the Astoria elevated to LaGuardia Airport, as well as making the light rail system compatible with the subway or LIRR to allow possible future interoperability.

One civic leader in Jamaica was optimistic that the people mover would spur development in that neighborhood,[56] and other supporters said it would benefit business and alleviate Van Wyck Expressway traffic in the long run.

[57] On the other hand, two community boards and several civic groups claimed the people mover would worsen traffic,[57] and local newspaper Newsday criticized the proposal as being ineffective without a direct link to Manhattan, citing the failure of the JFK Express.

[61] The Port Authority awarded a $930 million design–build–operate–maintain contract in April 1998[61][62] to AirRail Transit Consortium, a group composed of Slattery Skanska, Bombardier Transportation, STV Inc., Perini Corporation, and numerous consultants.

[69] Members of the New York City Planning Commission approved the condemnation of several buildings along the route in May 1999 but voiced concerns about the projected high price of the tickets, ridership demand, and unwieldy transfers at Jamaica.

[72] Although City Council speaker Peter Vallone was publicly neutral on the project,[73] his own office had published a study in early 1999, which criticized the AirTrain's lack of direct access to Manhattan and predicted that it would be of little help to the local economy.

[78] The Jamaica branch's location above the median of the busy Van Wyck Expressway, combined with the varying length and curves of the track spans, caused complications during construction.

[75][79] By the end of 1999, the columns in the Van Wyck's median were being erected,[80] and half of the viaduct spans had been built, although only fifteen percent of the system was finished at the time.

[70][83] Opponents claimed that the system had not undergone the Uniform Land Use Review Procedure process,[66] and more than 90 local organizations wanted the FAA to allow the public to discuss the PFC charges.

[88] In March, a federal judge vacated the project's approval because the FAA had collected and perused public comments after the public-comment deadline, but found that the PFC funds had not been misused.

[93] The advocacy groups filed a second federal lawsuit in 2000, claiming that the FEIS had included misleading statements about the effects of the elevated structure on southern Queens neighborhoods.

[99] In response to complaints, the Port Authority imposed strict rules regarding disruptive or loud construction activity, as well as implementing a streamlined damage claim process to compensate homeowners.

[138][139] The latter date was chosen to mark the centennial of the Wright Flyer's maiden flight, as well as to accommodate increased air traffic for the Christmas and holiday season.

[142] A writer for The New York Times said that, while the system was superior to the bus routes that it replaced, the AirTrain was "a complicated travel experience" that required a transfer, necessitated an additional fare, and lacked adequate signage.

[157][158] The Jamaica Center Mall, Joseph P. Addabbo Federal Building, the Civil Court, and a Food and Drug Administration laboratory and offices were all built in the five years before the AirTrain opened.

[171] U.S. senator Chuck Schumer had proposed a direct rail link from JFK Airport to Manhattan's Fulton Center the day the AirTrain opened.

[172] Between September 2003 and April 2004, several agencies, including the MTA and the Port Authority, conducted a feasibility study of the Lower Manhattan–Jamaica/JFK Transportation Project, which would allow trains to travel directly from JFK Airport to Manhattan.

[180] Shortly after Cuomo's announcement, the Regional Plan Association published an unrelated study for a possible direct rail link between Manhattan and JFK Airport.

[181][182] Yet another study in September 2018, published by the MTA, examined alternatives for an LIRR rail link to JFK as part of a possible restoration of the abandoned Rockaway Beach Branch.

[237] AirTrain JFK uses Innovia Metro ART 200 rolling stock and technology, similar to those used on the SkyTrain in Vancouver, the Everline in Yongin, and the Kelana Jaya Line in Kuala Lumpur.

[69] According to the FEIS, the system could accommodate over 3,000 daily riders from Manhattan, and its opening would result in approximately 75,000 fewer vehicle miles (121,000 kilometers) being driven each day.