On April 30, 2017, Cebgo planned to move out from Manila and transfer its main base to Mactan–Cebu International Airport in Cebu City because NAIA has already maxed out its capacity.

[6] The airline received its corporate registration from the Securities and Exchange Commission on March 25, 1995 mainly to operate aircraft leasing, chartering and a few domestic scheduled flights.

In May 1995, the airline was registered with the Clark Special Economic Zone to operate services in the Clark-Manila-Subic area and to tourist destinations throughout the Luzon and the Visayas regions.

On September 29, 2006, a deal was announced in which Singapore-based Tigerair would enter a commercial and operational tie-up with SEAir from February 2007.

It was then expanded to domestic destination from Manila (NAIA) to Davao and Cebu (slated to launch in July 2011).

However, the Civil Aeronautics Board (CAB) ordered the sales of the domestic flight under the partnership to be suspended on May 20, 2011, after receiving complaints from Philippine Airlines and Cebu Pacific.

Since the ban from CAB was lifted in October 2011, the planned domestic flight (between Manila (NAIA) to Davao and Cebu) was scheduled to start in May 2012.

[4] As of October 2024[update], Cebgo operates an all-ATR fleet composed of the following aircraft:[19][4] On June 16, 2015, at the 2015 Paris Air Show, Cebu Pacific announced orders for 16 ATR 72-600 aircraft, with options for 10 more, for its regional subsidiary Cebgo to meet growing demand for domestic services.