Notes:
Prices may have changed.
This was written for people who are visiting Japan for the first time.
If you like Kyoto, that’s awesome. You probably like chocomint ice cream too and that's OK. I love hiking there but avoid the city as much as possible.
I have had a love-hate relationship with Kyoto over the years as it has become very difficult to enjoy due to overcrowding so most of my trips there have been to the out-of-the-way places in recent years.
Kyoto has two subway lines and four railways. Additionally, there are two streetcar lines with next door Otsu adding another for a total of three. Inside the core of the city most of the places are best accessible by getting a bus from one of the major train stations. Google Maps has a good understanding of the bus and train routes. I have been using it recently to get around the city when I go. Take care to know which side of the road you need to be on to get the bus going in the correct direction. (I made that mistake a few years ago going to the Modern Art Museum with my daughter.)
There are various bus passes if you are going around the inner city and plan on riding the bus three or more times, the Kyoto City Bus one day pass is economical. I think it is around 500-600 yen. All the busses and trains also take the Icoca/PiTaPa or other Metrocard type prepaid IC card. Those cards are available at any JR Train station (2000yen: deposit of 500yen + 1500yen initial charge). Unlike some places, the rates do not change when you use the IC card. It is just easier to get on and off. If you do not have enough money on the card, you can pay the difference on exiting the station or getting off the bus.
1 Nijo Castle.
I went years ago as a student. Quite an amazing building and a good example of Japanese architecture and craftsmanship. You can combine this on a day with #3, #6, and #8. Just remember that it might be quite hot and humid even in October. Busses and major tourist places will be very crowded. This will be an enjoyable but tough day.
2 Fushimi-Inari Taisimha Shrine.
Due to its rating as the #1 attraction in Japan on TripAdvisor and the free entrance*, the number of visitors has skyrocketed. There are a few sections to the shrine. The entrance and up the hill a short way to the first pond is probably good enough if you want to combine this with #12 for a day out. Fushimi refers to the place this shrine is located. Inari refers to the fox deities that this shrine reveres. There are two fox statues in front of this shrine instead of the more typical “shisa” lions. Foxes are guardians of the rice storehouse and the key in the fox's mouth is to unlock the storehouse. This has come to mean that Inari shrines are good for business. You will find other Inari shrines across Japan and probably on your trip. Some large companies have an Inari shrine on their grounds. Some shrines to other Shinto deities have Inari Sub-shrines in them. I would recommend getting here very early in the morning to avoid the crowds (and the bus tours) then moving on to Uji for lunch and some touring there. See #12 for more information about combining these two places. There are not many good lunch options in the area.
*Shinto shrines, like Fushimi-Inari typically do not charge an entrance fee while some Buddhist temples, like Kinkaku-ji will. The “ji” and “tera” or “dera” means Buddhist temple. Shinto shrines are called “jinja” or “taisha”.
3 Kinkaku-ji: The Golden Pavilion.
The golden building is a reconstruction from the 1960s. Impressive if you like gold. The gardens behind the temple have always been more appealing to me but sadly hard to take in with the amount of people there.
4 Kiyomizu-dera Temple.
I would say this because of the difficult location, the long walk populated by hundreds of little gift stores and the construction going on meaning the view is greatly impaired by scaffolding. We went there as part of our temple pilgrimage route last year but it was difficult to enjoy the building for what it is. I would seriously skip this and visit Hase-dera in Nara instead if you want to see the similar style of deck architecture.
5 Sanjūsangen-dō Temple.
Amazing place. This was also on our temple pilgrimage route so we visited here after Kiyomizu-dera. It was very calm and serene after the previous hectic experience. Unless you know about and want to see the Buddhist statuary in the treasure hall (separate entrance fee), I would skip this along with #4 and #9 all together.
6 Kyoto Imperial Palace.
I went years ago and enjoyed it. Need to go again. Could combine with #1, etc. on a downtown route.
7 The Kyoto National Museum and Municipal Museum of Art
I would go depending on the current show and your interest in what is showing. It can be extremely crowded and have a long wait to enter. If there is a wait, I would skip it.
8 Gion’s Geishas and Temples
It has been hard for the Geishas recently due to all the photographers. This neighborhood has very much become a simulacra of what it once was. More of a Kyoto if done by Disneyland or like Times Square in New York. Please do not disturb the geisha (maiko) by taking photos as they walk around the neighborhood
9 Arashiyama
Worth checking out especially if you can get there around 7AM before all the shops open or 5PM after they close. The bamboo forest is smaller than you think it will be. I have not been to the Monkey Park but I have seen coupons for it at Hankyu Arashiyama station. The Randen streetcar is a joy to ride for any train enthusiast as is the Sagano Scenic Railway. I have not been on the latter, but have hiked in the hills above the tracks. Arashiyama is a good place for Kyoto souvenir shopping.
10 The Byōdō-in Temple
Highly recommended. This is located in Uji, the green tea village. This temple is printed on the 10yen coin so you will see people holding the coin up and taking photos of the main hall. There is a Uji-Fushimi Inari day pass on Keihan Railways to visit both places. You can make a day out of doing Fushimi-Inari in the morning and Uji for lunch and the afternoon. There is a park along the river that runs out of the mountain in Uji. If you arrive on Keihan, the train dead ends into the river. Most of the attractions are on the other side of the bridge and up the river to the left. If the weather is nice, I would even recommend getting a bento from a convenience store and having a riverside picnic. The Byodoin has two entrance fees. One gets you into the main ground, the second gets you into the main hall in a guided mini-tour. I highly recommend you do this. Inside the paint has dulled, but imagine yourself entering this hall before TV and mass media. The brightly colored halls were a very emotional experience for many. Like when people actually thought the train was going to fly through the screen in that old film reel. If you use the Keihan Uji ticket they give you a free postcard on entrance. That ticket also has some other small coupons around the village.
11 Ginkakuji-Kurama-Kibune
The top corner of Kyoto and a bit less crowded. I like hiking in the mountains up here but the routes are very steep and difficult. Doing the simple hike from Kurama to Kibune only takes a few hours and gives you a chance to sample nature in the Kyoto area.
There is a discount ticket for this trip if you are heading in from outside of Kyoto.
https://www.keihan.co.jp/traffic/valueticket/global/en/pdf/kyoto-kurama_kibune1dayticket-201603.pdf
Take the Keihan train to the last stop Demachiyanagi station. You can walk from there to Ginkakuji. It’s a pleasant walk not took long.
http://www.japanvisitor.com/japan-temples-shrines/ginkakuji-temple
Walk back (or bus) and get on the Eiden street car for Kurama (the Kurama ticket from Keihan works for this train line also)
http://www.keihan.co.jp/travel/en/plan-your-trip/itinerary-ideas/stroll-in-rakuhoku
Do this route from Kurama, up over the hill and back down to Kibune.
http://www.kotsu.city.osaka.lg.jp/library/ct/kikakujyousyaken/h26_kurama_kifune.pdf
https://www.insidekyoto.com/kurama-to-kibune-hike
12 Other places in Kyoto
Daigo-ji: Amazing gardens with very few non-Japanese tourists
Iwayamadera: In Otsu via JR or Keihan. Temple built around a very rocky hill.
Fukuchiyama: Up in the mountains a good 2 hours from Kyoto, but this little city has a rebuilt castle, great science museum, city zoo and botanical garden. Good place to experience rural Japan.
Amanohashidate: A pine lined sandbar about 2hrs or so from Kyoto city center. One of the 3 most beautiful views in Japan
The Kyoto Loop Hike. This hiking course loops around the city and can be done in 4 moderate to difficult full day hikes. Maps are in English and Japanese.
https://www.kyoto-trail.net/trail_course_e.html
Imakumanodera: Beautiful little shrine that is very peaceful and off the tourist routes.
Muko city Gekikara (super spicy) restaurant street: A bunch of restaurants that all have some insanely spicy items on the menus. Located between Kyoto proper and Osaka city.
http://kyoto-masters.com/en/taberu-2/get-your-body-and-soul-hot-with-super-spicy-gourmets-super-spicy-street-in-muko-city/