Company officials said Saturday that Michael Hickey will still have an "advisory role" after he steps down following decades with the airline.
He is the first senior executive to leave because of the damaging flight cancellations, which have disrupted travel plans for an estimated 700,000 passengers and undercut the company's bid to improves its customer service reputation.
The flights were cancelled because of holiday staffing and scheduling errors.
Ryanair chief executive Michael O'Leary said Hickey had made an "enormous contribution" to the airline in the last 30 years.
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.