Nico Bezuidenhout will take up the new role on August 1. He had previously spent 10 years running Mango, which is owned by South African Airways.
Fastjet chairman Colin Child said: "The board is delighted that Nico will be joining fastjet as chief executive. He brings strong commercial and strategic skills and a wealth of experience of operating a low-cost carrier.
“This experience, together with his detailed knowledge of the markets in which fastjet operates, will be invaluable to the company as it seeks to capture the growth opportunities in the region."
Bezuidenhout added: "I am very pleased to be joining fastjet at this stage in its development. Although market conditions are currently challenging, I am confident that we can build on the airline’s existing operational base to strengthen and develop the business and deliver on its considerable potential."
Fastjet has endured a tough time in recent months. Its share price has slumped following a series of profit warnings and it has come under a barrage of criticism from shareholder, and easyJet founder, Sir Stelios Haji-Ioannou.
Previous chief executive, Ed Winter, left in March and Haji-Ioannou also wants Child removed as chairman.
Commenting on the appointment, Haji-Ioannou said: “As they say, better late than never! Nico first appeared on a list of candidates put forward by a head hunter I had to hire last November. Colin Child has managed to procrastinate for seven months during which time fastjet burnt through another $25 million dollars. Colin Child is not the right man for the job of chairman.”