The closest Amtrak station to JFK Airport is New York Penn Station in Manhattan, which is the only Amtrak station in New York City. There are several options for continuing your commute to JFK:
Taxi/Uber/Lyft
Get a ride with Uber, Lyft or a taxi. The commute is 35 minutes to one hour depending on traffic.
Long Island Railroad/AirTrain
After arriving at Penn Station via Amtrak, transfer to the Long Island Railroad (LIRR) for a 24-minute ride to the Jamaica Station. Choose either the Babylon, Port Jefferson or Ronkonkoma lines. Check fares based on your departure day and time, and be sure to purchase your fare before boarding the train in order to save money. You can buy fare at Penn Station or via the MTA eTix app.
After arrival at the Jamaica station, there is a nearby connection to the JFK Airport’s SkyTrain (an additional cost and 10-minute ride).
Subway/AirTrain
Transfer to the E subway line in Penn Station and travel to Jamaica. The commute time is slightly longer, about 31 minutes, but the fare is cheaper.
What We Say
The cheapest option is the subway if saving money is important. Otherwise, if traffic isn’t too heavy, and money isn’t an issue, get a taxi, Uber or Lyft car. If you want a similar commute time as driving but without the expense, use the LIRR.
US Train Travel Guide 