The pilot managed to eject into the water and return to the HMS Queen Elizabeth, where they were based, after the crash at 10am on Wednesday.
A Ministry of Defence spokesperson said: “A British F35 pilot from HMS Queen Elizabeth ejected during routine flying operations in the Mediterranean this morning.
“The pilot has been safely returned to the ship and an investigation has begun, so it would be inappropriate to comment further at this time.”
The powerful F-35 Lightning warplane is believed to still be in the water after the first crash of its kind to happen to the UK’s flagship HMS Queen Elizabeth.
The £10million-a-pop aircraft were bought from the US in 2018 to be stationed on the £3.1billion aircraft carrier.
Then Defence Secretary Gavin Williamson said at the time: “These formidable fighters are a national statement of our intent to protect ourselves and our allies from intensifying threats across the world.
“With a game-changing ability to collect crucial intelligence, fight wars and tackle terrorism, these are the most advanced jets in British history.”
Jets from the vessel previously participated in strikes against the remnants of the so-called Islamic State in Iraq and Syria.
The jets are operated by the renowned 617 Squadron, also known as the “Dambusters” squadron.
Foreign Secretary Liz Truss spent time on board the vessel last month on the final day of her two-day visit to India.
Developers Lockheed Martin calls the F-35 the “most advanced fighter jet in the world”.
They say it comes in three variants — all single-seat jets.
They come in the form of the F-35A conventional takeoff and landing variant, the F-35B short takeoff/vertical landing variant, and the F-35C carrier variant to allow the jets to be used in any battle situation.