Fernandes, 59, a pioneer of Southeast Asia's budget carrier sector who is often compared to British tycoon Richard Branson, said in January that he intended to step aside within the next five years after more than two decades at the helm.
But Capital A, which operates budget airline group AirAsia, said in a statement he had signed a new five-year contract.
Fernandes said he was "excited to embark on the journey of completing the full transformation of Capital A."
The firm said it had approved an incentive package but did not reveal details.