The hybrid car-aircraft, AirCar, is equipped with a BMW engine and runs on regular petrol-pump fuel.
It takes two minutes and 15 seconds to transform from car into aircraft.
The certification followed 70 hours of flight testing and more than 200 take-offs and landings, the company said.
"AirCar certification opens the door for mass production of very efficient flying cars," its creator, Prof Stefan Klein, said.
"It is official and the final confirmation of our ability to change mid-distance travel forever."