[2][3] Filipino dentist Dr. Joel Mendoza established SkyJet Airlines in September 2005 as an air charter company offering flights aboard its fleet of British Aerospace 146 planes to group tourists going to the northern Philippine province of Batanes.

[5] In December 2013, SkyJet underwent a change in its corporate management after a group of investors led by entrepreneur and Cavite provincial board member Dino Reyes Chua took over the company.

In December 2016, Mendoza filed a syndicated estafa case against Tieng, Chua and several other officials of SkyJet for allegedly conspiring to defraud him of his shares in the company.

[25][26][27] On 18 May 2015, the CAAP suspended SkyJet's air operator's certificate due to various safety shortcomings on the rules and standards prescribed under the Philippine Civil Aviation Regulations (PCAR).

[28][29] SkyJet filed a case against the CAAP for the abrupt suspension, which it said was "irregular, not valid, and issued without due process of law", and sought PH₱20 million in damages.

[33] On 16 July 2018, the Bureau of Customs ordered the forfeiture of one of SkyJet's BAE 146-100 planes after the airline failed to pay PH₱90 million in duties and taxes to the government since its importation.

[34][35][36] In February 2020, SkyJet received a leased ATR 72-500 from Elix Aviation Capital to replace the aircraft that the government confiscated as it moves forward with its expansion plans.

According to an initial report of the Civil Aviation Authority of the Philippines (CAAP), the plane overshot the runway when it was landing and ended up in a field east of the airport.