Kyoto is the biggest name in Japan. Most of you will visit Kyoto. JR Kyoto station is probably the first step to Kyoto for you. There are so many trains, such as Shinkansen, Limited Express Haruka from Kansai airport, Limited Express Thuderbird to Kanazawa, commute trains to Osaka, Kobe and Nara, Kintetsu train, Kyoto city subway and many many more to depart and arrive in this station.
Train system in Kyoto may be complicated for you. There are three types of railway, JR, Kyoto City Subway and Private company’s railways. Actually it’s a key to travel in Kyoto smoothly and avoid wasting your valuable time. Of course city of Kyoto has city wide bus service. But during peak season, bus service runs behind the schedule sometimes due to traffic congestion.
And also, there are many types of deals, such as ICOCA, Kansai Thru Pass, JR Pass, Kansai Area Pass, Kyoto city pass. Each pass has different conditions. You have to understand which train system is covered by your pass.