Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Québec City to Kyoto as you normally would.
For a flight from Québec City to Kyoto, you will be flying from Quebec. Québec City (YQB) is just 13.5 km from the centre of the city. Quebec is the only Québec City airport and it handles 0 outbound flights to Kyoto per day. 0 airlines have flights to Kyoto from Québec City on a regular basis.