Kyoto's rail network is sparser than Tokyo's, which surprises a lot of first-time visitors — many of the biggest sights, including Kiyomizu-dera and Kinkaku-ji, aren't within easy walking distance of a train station. Buses do most of the work here, which changes how you should plan your days.
The bus network
City buses cover almost everywhere a visitor wants to go, run frequently on tourist routes, and use a flat fare within the central zone. The trade-off is crowding: routes to Kiyomizu-dera, Gion and Arashiyama get genuinely packed in peak season and at peak times (late morning through afternoon). Boarding at the rear and paying on exit is standard on most routes — watch what locals do if a route looks unfamiliar.
Subway and trains
Kyoto's two subway lines (Karasuma and Tōzai) are fast, uncrowded relative to buses, and useful for crossing the city quickly, but they don't reach many of the eastern hill sights directly. The JR Nara Line is the easiest way to Fushimi Inari and onward to Nara; the Keifuku (Randen) tram is a scenic, low-key way into Arashiyama.
IC cards: Icoca and friends
An IC card (Icoca is Kyoto/Osaka's version; Suica and Pasmo from Tokyo work identically here) is tap-in, tap-out on every bus, train and subway in the city, and also works at convenience stores and vending machines. Load it once, top it up as needed, and skip working out cash fares for every ride. If your phone's wallet already supports Suica, you may not need a physical card at all.
Cycling
Kyoto is largely flat and increasingly bike-friendly, and a rental bicycle can be the fastest way to combine several sights in one area — Arashiyama in particular rewards it. It's less practical for crossing the whole city or for the steeper lanes around Higashiyama's temples.
Taxis
Metered and easy to flag or queue for near major stations and hotels, taxis are a reasonable option late at night or for groups of three to four splitting the fare, but not a practical way to see the city all day given Kyoto's traffic in peak season.