The geography matters more at night
Mactan-Cebu International Airport is on Mactan Island, and the airport authority describes it as connected to Cebu City by the Mactan-Mandaue bridge and the Marcelo Fernan bridge.
That is the single most important thing to have straight before a late arrival. If your accommodation is a Mactan resort, you are a short ride from the terminal. If it is in Cebu City, you are crossing to the mainland. Those are different journeys, and knowing which one you have booked prevents a confused conversation with a driver at one in the morning.
The upside is real: at night, that crossing is far quicker than the same trip in daytime traffic.
Do these before you fly
Three preparations do most of the work.
Register for eTravel and save the QR code offline. It is the government's arrival registration, it is free, the guidance is to complete it within 72 hours before arrival, and the official site is the only one to use. Loading a QR code on airport wifi with a queue behind you is a bad start to a late night.
Book accommodation and confirm it accepts late check-in. Message the property with your flight number and expected arrival time. Some places have a night desk and some do not, and finding out at 1am is the wrong time.
Sort connectivity. Philippine law requires SIM registration, and for tourists that means a passport, a Philippine address and a return ticket. Airport SIM counters keep their own hours. An eSIM bought before departure removes the whole question, and the networks list traveller products designed for exactly this.
On the ground
Get pesos before leaving the terminal. Aim for small notes, because a driver at midnight may not have change for a large one, and that is a common friction point.
Then take a ride from an official point. The airport publishes its taxi services on its own site, and the general discipline applies: use the marked stands rather than accepting an offer from someone approaching you, and have your destination written down or shown on a map rather than pronounced.
If you use a ride app, check the plate against the booking before you get in, and note that airports usually designate a specific pickup bay rather than allowing pickup anywhere at the kerb.
If your onward plan is a ferry or a domestic flight
A late arrival followed by an early onward departure is a demanding combination, and worth thinking through rather than improvising.
Ferry terminals and domestic check-in counters run their own processes with their own queues, and a couple of hours of sleep between them rarely helps anyone. If your onward leg is early, consider staying near the airport rather than travelling into the city and back out.
If the onward leg is a sea crossing, remember that weather can disrupt it independently of your own timing, so a plan with no slack in it is fragile in the rainy months.
A short arrival checklist
eTravel saved offline before boarding. Accommodation confirmed with the property, including late check-in and its address written down. Cash withdrawn at the terminal in small notes. Connectivity sorted before you fly, or a counter identified as a fallback. An official taxi or a booked ride, with the plate checked. Then let the empty roads do you a favour.