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Few of Kyoto's tourist attractions are located close to subway or train stations. Instead, Kyoto has a dense bus network with direct bus lines from Kyoto Station and/or the city center around Shijo-dori (4th Avenue) and Kawaramachi-dori (Kawaramachi Street) to most major sights.
Kyoto is served by multiple bus companies. For central Kyoto, the green Kyoto City Bus buses are most numerous and useful. The red buses by Kyoto Bus are second most prominent and tend to be convenient to access sights in more outlying areas of the city.
The tourist offices provide a useful English network map for the Kyoto City Buses, which makes it quite easy for foreign visitors to access tourist attractions by bus. Despite the good map and English displays and announcements, however, getting off at the correct bus stop can still be stressful, especially in crowded buses.
Since buses are small and operate surprisingly infrequently even on some major routes, buses to major tourist sights can often get crowded, especially on weekends and during holidays. In addition, much time can be lost when buses get stuck or only proceed slowly in the busy street traffic. Consequently, it is recommended to use subways and trains as much as possible, and use buses only for medium and short distances, for example, from the closest subway station to the destination.
Buses are entered through the back door and left through the front door. The fare has to be paid when leaving the bus. Inside much of central Kyoto, there is a flat rate of 220 yen per ride. Outside the flat fare zone, the fare increases with the distance.

http://www.city.kyoto.jp/koho/eng/access/transport.html

There are two subway lines in Kyoto, the Karasuma Line which runs from south to north along Karasuma-dori (Karasuma Street) and stops at JR Kyoto Station, and the newer Tozai Line which runs from east to west and crosses the Karasuma Line at the intersection of Karasuma-dori and Oike-dori.

All JR lines including the Tokaido Shinkansen pass through or commence at JR Kyoto Station. JR trains are a good option for accessing the Arashiyama area (Sagano Line) and some attractions in southern Kyoto along the JR Nara Line, e.g. Fushimi Inari Shrine and Byodoin in Uji.

Kyoto is probably the Japanese city with the highest concentration of taxis. Especially in the city center, taxis are found everywhere. Taxis can not only be a more comfortable, but also an economical alternative to buses on short to medium distances for groups of three or more people.
Most taxis accommodate up to four passengers (not including the driver), while larger vehicles are able to accommodate an additional fifth passenger. The rate starts around 650 yen for the first two kilometers and increases by 80 yen for every additional 300-400 meters traveled.

Cycling is an excellent way to get around Kyoto. Bicycles can be rented from the following places


1) Kyoto Cycling Tour Project: Shops near Kyoto Stn. and 2 other key areas and they will also deliver bikes to your hotel/ inn;; Tel: 075-354-3636.


2) Passione: A rental bike shop owned by exbike racer (he speaks English!). Enjoy cycling around Kyoto with top quality bikes;; 9:00-18:00.


Rules and Tips for Cycling in Kyoto
Traffic rules are often different from what you are used to at home: Here are some rules and tips to make your cycling in Kyoto safer and more fun!

1) In Kyoto, as is true of most in most Japanese cities, there are few bicycle paths. Therefore bicycle on sidewalks with pedestrians on big, busy roads. Side streets are always better than main roads for safety and sightseeing.

2) Riding a bicycle after drinking is prohibited (and may be fined 20,000 yen)

3) Do not leave your bicycle on major streets in the downtown core;; Especially around busy subway/train stations. Kyoto City staff frequently remove illegally parked bicycles which have to be retrieved in distant locations plus payment of a fine (2,300 yen/bike). To be safe look for bicycle parking garages (on Kiyamachi, north of Shijo;; in Nijo Station;; in Demachiyanagi Stn.)

4) Bicycle riding is prohibited on some downtown streets. Follow the signs and push your bicycle on these streets.