Being the premier tourist city on Japan, Kyoto has over 1000 hotels with room prices generally ranging between ¥6,000 and ¥12,000 a night ($55 - $110 USD). At the higher end, luxury hotels rent rooms from ¥20,000 and up. If you book on your own, try to get a room near Karasuma Oike or Karasuma Shijo Stations. The next best location is the Kyoto Station area.
There are also hostels, guest houses and capsule hotels that offer rooms at the ¥2000-¥3000 yen range, but these should be booked early. They also tend to be less convenient. For these special deals, do online searches yourself. A couple possibilities are:
K's House Downtown Inn Kyoto Guest Hs Yululu Bird Hostel
Despite the large number of hotels, they are often booked up early, so we have reserved over a hundred rooms near Karasuma Oike Station through the Japan Tourist Bureau. Their rates are reasonable and they will provide good service.
Make JTB hotel reservations here: