Flight LS189 departed around 7am, and was scheduled to land on the Balearic island at 11am.
But after signalling an emergency, the Boeing 737 returned to Glasgow after entering a holding pattern.
Jet2 confirmed that the aircraft was suffering ‘pitch control issues’, which affect how the plane flies.
The aircraft, which made its maiden flight in 1998, was involved in a previous incident at Funchal Airport in Madeira, Portugal in 2014 and needed repairs after a tail strike during windy conditions.
The Boeing 737 can carry up to 189 passengers and seven crew.