Pilot lehin Pehlivan, 59, lost consciousness at some point after Flight TK204 took off from Seattle Tuesday night, Turkish Airlines spokesperson Yahya Üstün said in a statement.
Crew members decided to make an emergency landing and worked to revive the pilot, Üstün said, but he died before the plane landed.
Data from the tracking site FlightAware shows that the Airbus A350 landed at John F. Kennedy International Airport just before 6 a.m.
Arrangements were being made for passengers to reach their destination from New York, the airline spokesperson said.
Pehlivan had worked at Turkish Airlines since 2007, Üstün said. A routine health check in March showed no health problems that would have prevented him from working, he said.
"As Turkish Airlines, we deeply feel the loss of our captain and extend our sincerest condolences to his bereaved family, colleagues, and all his loved ones," Üstün said.