Flybe chief executive Christine Ourmieres-Widener will step down from her role on 15 July.
It follows the sale of Flybe to the Connect Airways consortium earlier this year, comprising Virgin Atlantic, Stobart Group and Cyrus Capital.
The deal is awaiting final competition clearance, expected this summer.
Flybe says it expects to be announce Ourmieres-Widener’s successor prior to her departure to “ensure a smooth handover”.
Flybe director Jonathan Peachey said: “On behalf of the entire Flybe board, I want to extend my gratitude to Christine for her commitment and significant contributions to Flybe.
“This includes her tireless efforts to safeguard the future for the customers and communities who rely on Flybe, as well as the company’s employees, its pension fund members and its creditors. We all wish Christine the very best for the future.”
Ourmieres-Widener added: “It has been a privilege to lead Flybe over the past two years and to work with such an outstanding and dedicated team of professionals.
“Together, we have been able to secure the jobs of our loyal Flybe employees with the sale to Connect Airways and provide our customers and the UK with the vital transport and travel infrastructure they rely on, while preparing Flybe for a bright future under its new ownership.”