As a codeshare partner of Philippine Airlines, PAL Express operates as a full service carrier within a low-cost model.

[7][needs update] Air Philippines was incorporated on February 13, 1995, with its hub at Subic Bay International Airport.

In September 1998, the airline was temporarily grounded by the Air Transportation Office (ATO), the forerunner to the Civil Aviation Authority of the Philippines (CAAP).

In March 1999, Air Philippines was granted approval to operate international services to Hong Kong, Japan, South Korea, Taiwan, and the USA.

[10] Air Philippines has said that they chose to back out of the Mabuhay Miles program to benefit their passengers, so rather than flying numerous flights to gain miles and wait to a certain point to receive bonuses, passengers can benefit with lower fares and more discounts with quicker bonuses, much more like today's modern-day low-cost airline.

[11] PAL announced on April 13 that the new fleet would be based mainly in Cebu to serve regional routes, while flights from Manila would also be launched.

The airline then announced that it would serve 22 inter-island routes, including some provincial points that lacked air service.

The airline restored jet service to Iloilo, Bacolod, Puerto Princesa and Cagayan de Oro, utilizing Airbus A320 aircraft.

[15] In January and early February 2012, GE Capital Aviation Services Limited (GECAS) announced the delivery of three new Airbus A320 aircraft to Airphil Express to help the carrier expand its fleet.

[19] On December 16, 2016, PAL Express began its Caticlan, Busuanga and Basco services from its Clark hub.