The Boeing 757 flight from Manchester to the Portuguese island of Madeira was diverted to Porto where it landed safely on Monday morning.
Passenger Nicholas Banks told Mail Online an announcement went out that there had been an incident on the flight deck, whereby the stand-in pilot came forward.
In a tweet, Jet2.com said the flight had been diverted to Porto due to an “onboard medical situation”.
A spokesperson said the first officer was able to land the aircraft as usual. The pilot was taken to hospital as a precaution.
The airline later issued a statement: “Flight LS765 from Manchester to Funchal diverted to Porto as a precautionary measure this morning, due to one of the pilots feeling unwell.”
It added a standby aircraft and replacement crew would be flown to Porto to get passengers on their way.