Between 1999 and 2008, the airport hosted no commercial flights. Proposal were made to reintroduce commercial service the airport, such as an independent Manila-Cauayan route, as well as a route further on to Tuguegarao Airport in Tuguegarao City. After almost a decade of not hosting commercial service, Cauayan Airport re-opened to commercial traffic on August 15, 2008 using PAL Express aircraft, marking the return of Philippine Airlines to Cauayan, having stopped its services to the city in 1994. At present, Cebu Pacific uses Airbus A319 for its Manila-Cauayan-Manila route.
Cauayan Airport was the airport of origin and destination for two fatal incidents in Philippine aviation: Philippine Airlines Flight 215 en route to Manila and Asian Spirit Flight 100 en route from Manila. Notably, it was Asian Spirit Flight 100 that forced the closure of the Manila-Cauayan route in 1999.