Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Cebu City to Machu Picchu as you normally would.
Cebu City Mactan Intl (CEB) is the airport you will fly out of if you book a flight from Cebu City to Machu Picchu. You should not have trouble finding flights to Machu Picchu from Mactan Intl; the airport handles an average of 0 outbound flights to Machu Picchu per day. You should also have plenty of airline options to choose from since 0 airlines have flights from the Cebu City airport to Machu Picchu. It is only a 7.6 km journey to Mactan Intl (CEB) from Cebu City’s city center.