[10][11] The airline has often been criticized for its frequent flight delays and cancellations, some without explanation, as well as alleged poor customer service, prompting investigations by the Philippine government.

In the 2000s, Cebu Pacific was granted rights to operate international flights to the region, including Malaysia, Indonesia, Singapore, Thailand, South Korea, Hong Kong, and Guam.

[18] Following this, Cebu Pacific experienced significant passenger growth, hiking up its sales volume by ninety percent.

[23] In April 2008, Cebu Pacific launched direct flights to its first two destinations in Vietnam: Hanoi and Ho Chi Minh City.

[25] In late 2007, Cebu Pacific announced plans to launch non-stop flights to the United States West Coast, Houston, and Chicago by mid-2009.

[26] Cebu Pacific's plans to begin international flights from Clark in 2007 were initially unsuccessful when its request was denied.

The nations involved came to an agreement that Cebu Pacific would be only allowed to operate charter flights from Clark to the respective countries' airport(s).

[32] In October 2010, the airline completed an initial public offering of 30.4% of outstanding shares, raising ₱23.3 billion prior to an exercise of an overallotment option.

[39] After taking delivery of its first two Airbus A330-300s, Cebu Pacific commenced international long-haul flights on October 7, 2013, to Dubai.

[40] Between 2014 and 2015, it launched flights to more destinations in the Middle East, including Kuwait City,[41] Doha, Dammam, and Riyadh.

[45] On June 1, Cebu Pacific revealed its new logo that represents the colors of the Philippines and also symbolizes as an evolution of a low-cost pioneer.

Due to low passenger demand, the airline laid off 1,300 employees that year,[52] and sent fourteen aircraft to indefinite storage in Alice Springs.

[62] The airline focused instead on expanding regionally within a five-hour radius, launching flights to secondary cities in Southeast Asia.

[62] As part of its regional expansion, it started flying thrice weekly to Da Nang on December 7, 2023,[63] and Chiang Mai on October 29, 2024.

WorldPerks offered regular travelers the ability to obtain free tickets, first-class upgrades on flights and other types of rewards.

[73] In April 2005, Aviation Partnership Philippines (A plus) was initially formed as joint venture of Singapore Airlines Engineering Company and Cebu Pacific to provide line and light maintenance service and started its operation in July of the similar year.

[77] On March 2018, Cebu Pacific created the 1Aviation after Manila International Airport Authority (MIAA) did not renew the contract of MIASCOR Ground Handling Corp due to series of luggage theft involving the subsequent staffs.

[82] The airline also signed a five-year agreement with Shell Aviation that would supply 25,000 metric tons of SAF to Cebu Pacific.

[84] On October 19, 2023, Cebu Pacific signed another five-year agreement with Neste, one of the largest producers of sustainable aviation fuel.

In addition to its CAPA Gold rating, CEB improved its S&P Global ESG Score to 41 in 2023 from 38 in 2022, ranking in the 69th percentile among the 63 airlines assessed by the international financial market intelligence provider.

[94] In September 2004, Cebu Pacific signed a purchase agreement with Airbus for the acquisition of twelve A319s and the lease of two A320s to replace its existing fleet of Boeing 757-200 and McDonnell Douglas DC-9 aircraft.

[101][102] In 2007, the airline ordered six Airbus A330-300s for use on long-haul Middle Eastern destinations such as Dubai as well as high-density regional flights.

[105] After initial deliveries in 2017 were delayed due to problems with the Pratt & Whitney PW1100G-JM geared turbofan engines,[106] it ordered seven A321-200s on June 7, 2017.

[110] On June 18, 2019, Cebu Pacific ordered 31 Airbus aircraft at that year's Paris Air Show, consisting of five A320neos, sixteen A330-900s,[111] and ten A321XLRs, in a deal worth US$6.8 billion at list prices.

[115] To prepare for the anticipated doubling of travel demand in Southeast Asia, Cebu Pacific sent requests for proposals to Airbus and Boeing in October 2023 for an order 100 to 150 aircraft.

[121] Cebu Pacific has been criticized for its poor passenger service, alleged overbooking, as well as flight delays and cancellations without any verifiable reason.

[124] In January 2018, Cebu Pacific was named as one of the world's least punctual airlines, with an on-time performance of 57.6 percent in 2017 based on data from OAG.

[125] During the "Super Pass" voucher sale in March 2023, Cebu Pacific was criticized for system glitches that caused transaction errors and additional charges.

The airline blamed on supply chain issues and grounded aircraft as a result of the disruptions, and apologized to affected passengers.