Ten flights a week will be operated to Roxas, while 17 weekly flights will service Kaibo from the Philippines’ capital.
Passenger capacity will increase on the Manila-Roxas route by 42.8 percent once the changes take effect, while the capacity on flights to Kaibo will rise by 25 percent.
The airline explained that will "continue to expand its domestic operations", which will allow passengers to benefit from improved connectivity and a more convenient schedule.
It also said that it would offer the "lowest all-inclusive fares" in order to support both tourism and trade in the Philippines.
Cebu Pacific announced last week that its flights to Bangkok from both Manila and Clark would operate as scheduled.
In addition to its 31 domestic destinations, the carrier operates flights to 15 cities throughout the Asian continent.
Having been established 14 years ago, Cebu Pacific has the youngest fleet of aircraft in the Philippines.