The airline is a subsidiary of JG Summit Holdings. Cebu Pacific is currently headed by Lance Gokongwei, presumptive heir of John Gokongwei, the chairman emeritus of JG Summit. As of January 2013, the company has 3,297 employees. 2,565 were from operations, 429 from the commercial departments, and 303 from the support departments. In October 2010, the airline completed an IPO of 30.4% of outstanding shares.

In 2010, Cebu Pacific became the Philippines' largest airline based on number of passengers flown on domestic and international routes. According to Civil Aeronautics Board data, Cebu Pacific flew 2.45 million total passengers in the first quarter of 2010, nearly 110,000 more than Philippine Airlines, which carried 2.34 million systemwide during the same period.

The airline was established on 26 August 1988, and started operations on March 8, 1996. Republic Act No. 7151, which grants franchise to Cebu Air, Inc. was approved on 30 August 1991. Cebu Air, Inc. was subsequently acquired by JG Summit Holdings (owned by John Gokongwei). Domestic services commenced following market deregulation by the Philippine government. It temporarily ceased operations in February 1998 after being grounded by the government due to an accident, but resumed services later the next month following re-certification of its aircraft. It initially started with 24 domestic flights daily among Metro Manila, Metro Cebu and Metro Davao. By the end of 2001, its operations had grown to about 80 daily flights to 18 domestic destinations.

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