The airline based in Exeter have sponsored the football club since the summer of 2003, the beginning of Exeters first season in non-league football.
During that time City have played at Wembley twice, been promoted twice and played Manchester United and Liverpool in cup matches in front of huge TV audiences.
The value of the shirt sponsorship deal has not been disclosed, but it is believed to be less than the £53 million a year reportedly paid by Chevrolet to Manchester United or the £25 million a year Liverpool receive from Standard Chartered bank.
Mark Jenkins, head of commercial at Exeter City, said: “We are delighted that Flybe are backing us again for another two seasons.
“This is one of the longest standing corporate sponsorship for a current Football League club and underpins Flybe’s dedication to the club. It is great to still have such a household name proudly displayed on the front of our kits and we are looking forward to a successful season for both city and Flybe.”
Julian Tagg, Exeter City’s chairman, added: “I would like to thank Flybe for their continued support; the longevity of their sponsorship has been vital in enabling our community owned club to become stable and to grow over the years.”
Phil Delaney, Flybe director of sales and marketing, said: “We have enjoyed a fantastic relationship with both the club and the fans over the past 13 years and are looking forward to continuing that into the future.”