The F/A-18, one of 32 belonging to the Swiss armed forces, was flying in airspace shared by the Swiss and French for training exercises when it came down in an uninhabited area east of the French city of Besançon, the Swiss federal department of defence, civil protection and sport (EDVBS) said in a statement.
The 38-year-old pilot, who was the only one on board, ejected prior to the crash and was taken to Besançon hospital for treatment of his injuries.
No one on the ground was injured.
The American-made F/A-18, which took off from the town of Payerne in the Swiss canton of Vaud, was simulating aerial combat with two F-5 Tigers, Daniel Reist, a spokesman for the EDVBS, told Swiss broadcaster RTS.
Though the cause of the crash is not yet known, a collision between the planes has not been ruled out, said Reist.
Aldo Schellenberg, head of the Swiss air force, told RTS that an agreement with the French allows such exercises to take place in the area several times a month.
Speaking to news agency AFP, a witness to the crash said that he heard “a loud bang” which was followed by a short outage of electricity.
Around the crash site he saw “a big hole and smoke”.
This is the third crash involving an F/A-18 in Switzerland after accidents in Crans-sur-Sierre in 1998 and Lopper in 2013.