Check-in at the airport counter is free, but Cebu Pacific is trying to get passengers to check in online and usually only a few counters are open, so there are long lines.
Online check-in is available from 72 hours to 4 hours (up to 2 hours for domestic flights) before departure. Just print out your boarding pass if you have luggage, and drop it off at the airport's "Drop-off" express counter.
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