Flight LS875 from Manchester to Faro took off at 08:39 but was then put in holding, drifting above the city trying to burn fuel until it was light enough to land.
The plane is the same Boeing 757-200 that had similar gear issues two days ago, when it circled over the city for 90 minutes. Wednesday's flight, which was originally bound for Greece, also landed safely.
Jet2 is a low-cost airline based at Leeds Bradford Airport. The carrier is owned by London-listed Dart Group.