A spokesman for the Federal Aviation Administration, Jim Peters, said flight 2921 landed safely shortly before 9 a.m., about an hour after it departed.
It wasn't clear how many people were on board.
No injuries were reported.
Michael Thomas, a spokesman for Endeavor Air, which was operating the flight, said the crew followed established procedures and opted to return to JFK after noticing the smell. The passengers were taken off the plane and transported them to the terminal, where they boarded another plane.
"Safety is always Endeavor Air's top priority," Thomas said.
The investigation is ongoing.