Sir Timothy Anderson, whose position will be effective from October 15 but who will join on a part-time basis from August 1, will become a member of executive committee.
Luke Farajallah, the current chief operating officer will be leaving on October 31.
Anderson has been a non-executive director on the Flybe board since May 2014 and has chaired the group’s safety and security committee during that time.
He will stand down from the board on July 31 to enable him to prepare to take up this executive appointment with the company.
Prior to joining Flybe, Anderson had a career in the Royal Air Force.
Christine Ourmieres-Widener, Flybe chief executive, said: "I am delighted that Timo has agreed to join our executive team.
“His wealth of experience in aviation, logistics and safety will be invaluable to us, building on his past four years on the board. He brings exceptional leadership, management skills, cost discipline and tremendous drive that will be key for us to deliver operational excellence.
“I would like to thank Luke Farajallah for his hard work and enormous contribution over the last three years and wish him well for the future.”