In a statement on its website, it said one of its former staff was facing legal proceedings while another "misused" company information on a flight on August 12.
"Cathay Pacific confirms that two pilots have been terminated in accordance with the terms and conditions of their employment contracts," the airline was quoted as saying by Efe news.
"Cathay Pacific wishes to make it clear that we express no view whatsoever on the subject matter of any ongoing proceedings."
The carrier gave no further information.
Chinese state media claimed that an anonymous poster uploaded a photograph on social media apparently from a cockpit of a Cathay Pacific plane urging protesters to continue their sit-in at Hong Kong's international airport, which for two consecutive days on August 12 and 13 brought flights to a standstill.
The other pilot in question is thought to be a person who was arrested during the protests and currently out on bail pending a court appearance in September to face rioting charges, which carries a sentence of up to 10 years.
The city has been gripped by 10 weeks of protests, which originally erupted over a controversial extradition bill that would have allowed China to pursue political dissidents and fugitives in the territory, which, since being handed back to Chinese sovereignty from the British in 1997, still retains a large degree of autonomy.
Hong Kong's Chief Executive Carrie Lam declared the extradition bill "dead" but it was not enough to quell the protests, which have morphed into catch-all demonstrations against the local government.
Throughout the beginning of the week, Cathay Pacific was forced to cancel 272 flight amid large-scale protests in the airport terminal building, affecting more than 55,000 passengers, the airline said.
Beijing has also started ramping up its warnings about the ongoing unrest in Hong Kong.
( With inputs from IANS )