Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Yogyakarta to Kyoto as you normally would.
If you book a flight to Kyoto from Yogyakarta, you will be flying from Adisutjipto, which is the city’s only airport. Yogyakarta Adisutjipto (JOG) is located 6.8 km from the centre of Yogyakarta. There are 0 flights from Adisutjipto to Kyoto per day from 0 different airlines.