Passengers say it's just another reason to leave extra time coming into and out of JFK.
Monday morning, work crews shut down the airport's largest runway for the four-month reconstruction project.
The runway, known to pilots and controllers as 13-right, 31-left, is nearly three miles long and handles roughly half the arrivals and departures at the busy airport.
The Port Authority is ripping up every inch of it, re-designing and re-paving it, with new taxiways intended to make the airport more efficient.
But the delays over the next several months could be substantial, up to one hour or more during peak hours.
Stephen Abraham is president of JFK's controllers' union.
"On good weather days, they'll notice a little, and on bad weather days, they'll notice a lot," he said. "Our delays could be hours, not minutes."
JFK is already notorious for flight delays, and some are skeptical that the project could drag into the peak summer travel months.
"New York's Kennedy Airport is already a nightmare," travel expert Joe Brancatelli said. "And since nothing ever runs on time, on budget or as expected in New York, you just know this can't have a happy ending. Of course, how much worse can it get?"
Several airlines, including JetBlue, have cut back their schedules to help minimize delays. But some industry experts predict that with fewer flights, prices are likely to climb.