American Airlines Flight 2681 to Cancun took off just after 1 p.m. and encountered an engine-related issue, the FAA said.
Port Authority police said there was a report of an engine fire. The Boeing 738 landed safely at JFK at 1:20 p.m.
"The crew declared an emergency after the flight departed Kennedy Airport due to an engine-related issue," the FAA said in a statement.
The Port Authority Police union posted a photo of the plane, saying there was no evidence of a fire.American Airlines said the plane will be checked out.
No one was hurt in the incident.