The F35B, a stealth fighter-bomber, made a conventional take-off and landing, and climbed to 15,000 feet (4,572 metres) for a series of handling, engine and other systems checks. It landed successfully after 46 minutes in the air.
Air Commodore Mark Green, MOD Joint Combat Aircraft team leader, said:
"This is a great achievement by Lockheed Martin, Northrop Grumman, BAE Systems, Pratt and Whitney and Rolls Royce - they should be congratulated for their endeavours.
"This programme is constantly breaking new ground, and with the first flight milestone behind us, we look forward to the demonstration and associated flight test of the aircraft's Harrier-like short take off and vertical landing capabilities in the coming months."
The supersonic stealth fighter-bombers will form the next generation of Navy and RAF jump-jets and the F35B is one of three variants of the US Department of Defense Joint Strike Fighter (JSF) project. The MOD is a partner in the JSF programme and is investing £1.8 billion developing the aircraft.
The F35B was flown by a British pilot, BAE Systems employee and former RAF Harrier pilot, Graham Tomlinson.
The Joint Strike Fighter is the aircraft of choice to fulfil the MOD's Joint Combat Aircraft requirement and fly off the two new Royal Navy aircraft carriers.