The airline, which was established by easyJet founder Stelios Haji-Ioannou in 2012, said this would result in a saving for the company over the next five years.
“This agreement represents a major step forward as the company continues with its stabilisation efforts under new management,” said the company in a statement.
Haji-Ioannou said: "Fastjet is a great brand in all its African markets, making it a highly valuable asset for the company.
“I have accepted the view of the current board that the company should own its own brand rather than licence it from me.