"We are banning shark fin carriage effective immediately as we learned that unsustainable shark fishing and our carriage of shark fin is not aligned with (our) position on sustainable development," the airline said in a statement.
The carrier, controlled by the Gokongwei family, an ethnic Chinese clan with interests in food processing, real estate and banking, also it would no longer serve shark fin soup in its corporate events.
Cebu Pacific, the country's largest airline in terms of number of passengers carried, becomes the second Filipino carrier to ban shark fin shipments following a similar decision by rival Philippine Airlines in April.
The fins are traditionally used in expensive Chinese soups and served at important events.
Conservationists warn that the demand for shark fins has led to overfishing, with many shark species now considered endangered.