It is possible to visit Koya-san from Kyoto in a single day, but this would make you spend quite a lot of time in trains. The total journey takes between 2:30 and 3:00 hours.
You have to first go to Osaka and then SHINIMAMIYA or NANBA, and from there take the Nankai Koya Line, which is not a JR line and therefore not covered by the JR Rail Pass, to GOKURAKUBASHI; a cable car will then bring you to Koya-san (not covered neither).
You have to pay 1230 yen per way for the Nankai Lines, more if you take a limited express with a reserved seat.
Check the timetables on Hyperdia :
http://grace.hyperdia.com/cgi-english/hyperWeb.cgi
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