Public transportation in Japan is clean, reliable, fast, and expensive. There are lots of transportation passes for tourists so I had to do a fair amount of research beforehand. These are the ones I actually ended up spending money on.
There are multiple train systems in Japan, the most common being JR. Different train systems have different passes. JR has multiple types depending on the area covered and duration. I bought the Kansai wide area pass for JPY 8500 (~USD 77). It covers Kyoto, Osaka, Himeji, Kobe, Kinosaki, and the Kansai airport for 5 days. A round trip to Kinosaki from Kyoto alone costs more than the pass itself, so it was a great deal.
For JR passes, you can reserve online and get a discount (JPY 500 ~ USD 5). When you make the reservation with intended travel dates, they email you which you need to print out and bring to a JR train customer service. I was able to get the physical pass from the Kansai airport JR customer service.
I bought some other train tickets separately. The general JR pass covers all region so I could have gotten that pass, but the pass itself is very expensive and the math told me no. I bought a Shinkansen (fast train) ticket from Kyoto to Tokyo for JPY 12100 (~ USD 110). I also got a Torokko ticket (scenic train between Kyoto and Kameoka) for JPY 620 (~ USD 6). There were also some other miscellaneous train tickets I bought separately.
You can use transportation card in most of the public transportation system, and it’s very convenient for subways, buses, and other short train trips. You can use the card at most of the convenience stores as well. Unfortunately, you can only use cash to charge the card.
SUICA seems to be the most popular since you can get them around Tokyo, but they have ICOCA, and not SUICA in Kansai region (Osaka and Kyoto). I think there are a few other cards similar as well. SUICA cards actually work with ICOCA system and vice versa. But if you are trying to return the card and get the refund, you can only return ICOCA card in Kansai region and similarly for SUICA card. I got ICOCA card since Kyoto was my first city.
There was actually a special version of ICOCA card while I was there, called Kansai One Pass. It looks prettier and has some discount perks at tourist attractions. Mine was a pilot program one so it costed JPY 3000 (~ USD 27) including JPY 500 deposit (so JPY 2500 was available for use). I think the current one only costs JPY 2000 with JPY 500 deposit.
Transit cards are very convenient since you don’t have to worry about change at convenience stores and train/subway stations. If you’re staying for a few days in Japan, I would definitely recommend getting one unless you plan on taking taxis everywhere.
Getting around Kyoto
Inside Kyoto the buses seemed to be the most common mode of transportation. You get on the bus first through the back door, and pay the driver when you get off through the front door. ICOCA cards work fine and a single fare is JPY 230 (~ USD 2). You can also buy the day pass from the driver, and it is JPY 500 (cash only). A day pass is a thin plastic card you insert into the machine instead of tapping.
Unfortunately bus stops were inaccurate on Google maps, so it was difficult to navigate around. Sometimes I would go to a “stop”on Google maps only to realize there isn’t one. Buses that stop at popular tourist attractions are very crowded, and at some point I had to pass on buses multiple times because they all arrived full. I ended up walking for half an hour to take a different bus. It could have been just me, but it was the least reliable in Japan from my experience.
Getting around Tokyo
I mostly took trains in Tokyo, and they felt more like subways than trains. The fare depends on the distance travelled. I don’t remember exactly what the price range was but in most cases, since I was staying near Tokyo station, it wasn’t too bad. The trains during rush hour were very crowded.
One thing that really struck me was how clean all the vehicles were. Coming from San Francisco I was very jealous. The shinkansen, especially, was very spacious and clean. As someone without a driver’s license, Japan was very easy to travel around.