Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Boracay to Kyoto as you normally would.
For a flight from Boracay to Kyoto, you will be flying from Godofredo P. Ramos. Boracay Godofredo P. Ramos (MPH) is just 5.5 km from the center of the city. Godofredo P. Ramos is the only Boracay airport and it handles 0 outbound flights to Kyoto per day. 0 airlines have flights to Kyoto from Boracay Godofredo P. Ramos on a regular basis.