From next month, the deal will also include ITV Meridian, its fifth regional sponsorship with ITV.
The airline already sponsors ITV's regional channels South West ITV, UTV in Northern Ireland, ITV Scotland and Channel Island TV.
Flybe is the biggest scheduled carrier at Southampton Airport, which is within the Meridian region.
The creative features Flybe's Exeter headquarters and shows a 118-seat Embraer 195 jet aircraft being tested against the elements.
The creative will support Meridian's weather bulletins 31 times each week.