The agency won the account after a competitive pitch process, which included Now and Leagas Delaney in the final stages. McCann was knocked out in an earlier round and Joint had talks with Flybe but declined to pitch.
The process kicked off in November, with pitches taking place in December.
New creative will launch in the spring, with a different positioning for the brand. Although the media plans are still being finalised, Flybe is expecting to invest in TV advertising. Digital, radio, press and outdoor are also being considered.
The Corner replaces leisure and travel specialist Souk Advertising. Flybe will continue to use Starcom as its media buying agency.
The process was led by Flybe’s director of marketing, Simon Lilley. He said: "The Corner has a new agency hunger, but also demonstrated to us an impressive blend of major brand and big agency experience. They clearly understood our business challenges and backed this up with a superior customer insight."
In November, the airline reported pre-tax profits of £13.8 million for the six months to 30 September, compared with a loss of £1.6 million a year earlier.
However, Flybe also announced it would make 500 redundancies across the UK and proposed closing six bases (Aberdeen, Guernsey, Inverness, Isle of Man, Jersey and Newcastle) as part of an £85 million cost-cutting plan.