Worawut Kongkositkul, who is in charge of flight operations for the airline, said Peter Esberte, who co-piloted flight SL8537 from Hat Yai to Bangkok, collapsed and was later pronounced dead.
He said the 47-year-old Dutch pilot died while he was being taken from the airport to a hospital. He could not confirm the cause of death.
Mr Worawut said Esberte joined the low-cost airline at its launch last year and was healthy with no record of health problems. His latest medical check-up in February and March showed no signs of problems, he added.
After Esberte collapsed, the pilot turned the plane around and landed safely at 1.21pm, he added.
Aeronautical Radio of Thailand (Aerothai) said Esberte died of a heart attack on the plane.
Thai Lion Air uses Boeing 737-900 aircraft on the service.
Civil Aviation Department chief Woradej Harnprasert said the problem began as the plane was 3,000 feet above the ground.
Flight SL8573 left Hat Yai at 12.15pm and was scheduled to land at Don Mueang airport at 1.45pm.
The flight eventually arrived at Don Mueang at 4.05pm. The number of passengers on the flight was unknown.