I plan to take a train from Jakarta to Yogyakarta but I wonder what is that the best way to get from Jakarta to Yogyakarta? Also, what are my options for the train?
In Java, the train system is well connected and fairly easy on travelers. It is one of the best way to get from Jakarta to Yogyakarta without much pain, and it is better than the bus because it skips the notorious traffic of Indonesia. You may choose from a few train companies that does direct train from Jakarta to Yogyakarta.
Check here at their Indonesia official train website (http://www.kereta-api.co.id/) for the timetable for the trains. Unfortunately, the site is only in Bahasa Indonesia (Indonesian) but you can read the names of the places, note that Tanggal is date, Stasiun Asal is From and Stasiun Tujuan is To.