The Port Authority could only use the funds from the Passenger Facility Charge to make improvements that exclusively benefited airport passengers.
As a result, only the sections linking Jamaica and Howard Beach to JFK Airport were approved and built, since it was expected that airport travelers would be the sole users of the system.
The federal government approved the use of PFC funds for the new light rail system in February 1998.
Some $200 million of the project's cost was not eligible to be funded from the PFC tax because, according to the FAA, the tax funds could not be used to pay for "any costs resulting from an over-designed system", such as fare collection systems.

Construction of the system began in May 1998.
Most of the system was built one span at a time, using cranes mounted on temporary structures that erected new spans as they progressed linearly along the structures.
Several sections were built using a balanced cantilever design, where two separate spans were connected to each other using the span-by-span method.
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.
One lane of the Van Wyck had to be closed in each direction during off-peak hours, causing congestion.

The route ran mostly along existing rights-of-way, but three commercial properties were expropriated and demolished to make way for new infrastructure.
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 logistics of the project.
These concerns included the projected high price of the tickets, ridership demand, and unwieldy transfers at Jamaica.

Though community leaders supported the project because of its connections to the Jamaica and Howard Beach station, almost all the civic groups along the Jamaica branch's route opposed it due to concerns about nuisance, noise, and traffic.
There were multiple protests against the AirTrain project; during one such protest in 2000, a crane caught fire in a suspected arson.
Homeowners in the vicinity believed the concrete supports would lower the value of their houses.
Residents were also concerned about the noise that an elevated structure would create, and according to a 2012 study, the majority of residents' complaints were due to "nuisance violations".
The Port Authority responded to residents' concerns by imposing strict rules regarding disruptive or loud construction activity, as well as implementing a streamlined damage claim process to compensate homeowners.
Through 2002, there were 550 nuisance complaints over the AirTrain's construction, of which 98% had been resolved by April of that year.
Not all community boards saw a high level of complaints; Queens Community Board 12, which includes the neighborhood of South Jamaica along the AirTrain's route, recorded few complaints about the construction process.

The Air Transportation Association of America (ATA) filed a federal lawsuit in January 1999 alleging misuse of PFC funds.
In March, a federal judge vacated the project's approval because the FAA had incorrectly continued to collect and make use of comments posted after the deadline for public comment, but found that the PFC funds had not been misused.
The FAA opened a second request for public comment and received a second approval.
In 2000, two local advocacy groups filed a second federal lawsuit, claiming that the FEIS had published misleading statements about the effects of the elevated structure on southern Queens neighborhoods.
The ATA and the two advocacy groups appealed the funding decision.
The ATA later withdrew from the lawsuit, but one of the advocacy groups proceeded with the appeal and lost.

By the time the appeal was decided in October 2000, two-thirds of the system's viaduct structures had been erected.
Construction progressed quickly, and the system was ready for its first test trains by that December.
In May 2001, a $75 million renovation of the Howar
The Port Authority could only use the funds from the Passenger Facility Charge to make improvements that exclusively benefited airport passengers. As a result, only the sections linking Jamaica and Howard Beach to JFK Airport were approved and built, since it was expected that airport travelers would be the sole users of the system. The federal government approved the use of PFC funds for the new light rail system in February 1998. Some $200 million of the project's cost was not eligible to be funded from the PFC tax because, according to the FAA, the tax funds could not be used to pay for "any costs resulting from an over-designed system", such as fare collection systems.
Construction of the system began in May 1998. Most of the system was built one span at a time, using cranes mounted on temporary structures that erected new spans as they progressed linearly along the structures. Several sections were built using a balanced cantilever design, where two separate spans were connected to each other using the span-by-span method. 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. One lane of the Van Wyck had to be closed in each direction during off-peak hours, causing congestion.
The route ran mostly along existing rights-of-way, but three commercial properties were expropriated and demolished to make way for new infrastructure. 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 logistics of the project. These concerns included the projected high price of the tickets, ridership demand, and unwieldy transfers at Jamaica.
Though community leaders supported the project because of its connections to the Jamaica and Howard Beach station, almost all the civic groups along the Jamaica branch's route opposed it due to concerns about nuisance, noise, and traffic. There were multiple protests against the AirTrain project; during one such protest in 2000, a crane caught fire in a suspected arson. Homeowners in the vicinity believed the concrete supports would lower the value of their houses. Residents were also concerned about the noise that an elevated structure would create, and according to a 2012 study, the majority of residents' complaints were due to "nuisance violations". The Port Authority responded to residents' concerns by imposing strict rules regarding disruptive or loud construction activity, as well as implementing a streamlined damage claim process to compensate homeowners. Through 2002, there were 550 nuisance complaints over the AirTrain's construction, of which 98% had been resolved by April of that year. Not all community boards saw a high level of complaints; Queens Community Board 12, which includes the neighborhood of South Jamaica along the AirTrain's route, recorded few complaints about the construction process.
The Air Transportation Association of America (ATA) filed a federal lawsuit in January 1999 alleging misuse of PFC funds. In March, a federal judge vacated the project's approval because the FAA had incorrectly continued to collect and make use of comments posted after the deadline for public comment, but found that the PFC funds had not been misused. The FAA opened a second request for public comment and received a second approval. In 2000, two local advocacy groups filed a second federal lawsuit, claiming that the FEIS had published misleading statements about the effects of the elevated structure on southern Queens neighborhoods. The ATA and the two advocacy groups appealed the funding decision. The ATA later withdrew from the lawsuit, but one of the advocacy groups proceeded with the appeal and lost.
By the time the appeal was decided in October 2000, two-thirds of the system's viaduct structures had been erected. Construction progressed quickly, and the system was ready for its first test trains by that December. In May 2001, a $75 million renovation of the Howar
AirTrain JFK