Tokyo to Kyoto by Train: Ultimate 3-day Itinerary
How to get from Tokyo to Kyoto? It’s easy to do a 3-day round trip by train from Tokyo to Kyoto and Nara, covering some of the most important cultural and political sites in the two former capitals. For the Tokyo to Kyoto 3-day itinerary, purchasing a Japan Rail Pass valid for 7 days (including the bullet train) may be the cheapest option. In addition to the 3-day trip to Kyoto, you will then be able to use it another 4 days to visit other places in Japan.
To get the most out of just 3 days in Kyoto and Nara, you need to prepare well – and have a clear idea of which historical sites, temples and shrines you want to see. Why not participate in a traditional tea ceremony (affiliate link) or a Geisha district walking tour by night (affiliate link)?
The easiest way to get around to all the temples and shrines in Kyoto is on foot. So although you can now and then take a bus, a local train or perhaps a taxi, you will most likely cover large distances on foot!
Also, try to limit your luggage for the Kyoto trip to a small backpack. Your hotel in Tokyo may well be willing to store your suitcase until you return to Tokyo. That way, you can carry your small rucksack around on Day 1 in Kyoto and Day 3 in Nara before returning to Tokyo by train. Alternatively, you may be able to leave your luggage in a locker at Kyoto Station – or leave it at your hotel/hostel near the station. That will add valuable time to your sightseeing in Kyoto and Nara!
Fushimi Inari Shrine in Kyoto, with the double torii rows | Photo: Travel In Culture
Out of the wide variety of historical sites and fascinating temples and shrines in Kyoto and Nara, choosing the right ones to visit is no easy task. In Kyoto alone, there are around 1600 temples and 400 shrines – so you will need to prioritise your sightseeing!
Below is a suggested itinerary for Kyoto and Nara, covering some of the most significant temples and shrines – and a few other curiosities. Of course, there are many other fantastic temple structures in Kyoto, which you might also want to include – but if you are limited by having only 3 days, at least this is a good starting point! It will be 3 long sightseeing days – but it is worth all the effort!
Nishiki Market | Photo: Travel In Culture
DAY 1: Tokyo-Kyoto by Train, Temples & Shrines in Kyoto
You start from Tokyo Station early in the morning by Shinkansen train. You can reserve a seat for the Tokyo-Kyoto train in advance – perhaps already when you arrive at the airport.
Travelling from Tokyo to Kyoto by Shinkansen is smooth and comfortable. On the way, you will pass Mount Fuji very close. With a bit of luck, you may be able to see the snow-capped mountain and its iconic, symmetrical shape quite clearly. The bullet train from Tokyo to Kyoto bores almost silently through the countryside. Sit back and enjoy the scenery.
If you have skipped breakfast to leave Tokyo early, you can do like the vast majority of train travellers who get bento boxes at Tokyo Station or elsewhere before boarding the train. These bento trays contain small compartments for a variety of culinary delights.
After some hours (usually between 2 hours and 40 minutes and 4 hours – depending on the type of Shinkansen train), you will arrive in Kyoto, where you will immediately (perhaps after getting rid of your luggage in a locker) begin your temple and shrine tour.
From Kyoto Station, you can walk directly to the centrally located Buddhist temple complex Higashi Honganji. The UNESCO World Heritage temple Nishi Honganji from 1591 is the head temple of the Buddhist Honganji creed and a fine example of a Buddhist temple with contemporary practice of Buddhism. The adjacent Higashi Honganji is most impressive in size and is the largest wooden structure in Kyoto.
The Buddhist temple complex Higashi Honganji has the largest wooden structure in Kyoto | Photo: Travel In Culture
Remember to take off your shoes and put them on the supplied rack before entering. During the colder times of the year, many of the temples provide visitors with slippers to wear while inside! The shelves are numbered, so it is easy to find your own shoes again!
Continue to the Sanjusangendo Temple. It dates back to 1164 and was constructed on the orders of the former Emperor Go-Shirakawa. It is famous for having 1001 carved wooden golden statues of Kannon, the Buddhist Goddess of Mercy. A gigantic wooden statue sits in the hall, flanked by 500 smaller statues on each side in ten rows. A Kannon has 11 heads and 1000 arms! It is quite an overwhelming sight in the long temple hall, Japan’s largest wooden structure.
Vermillion columns at Sanjusangendo Temple | Photo: Jarodsai / Pixabay
Next, head for the Kiyomizudera Temple from 780, also a UNESCO World Heritage Site. It is in eastern Kyoto on the green forest hills. The temple is a Buddhist construction belonging to the Hosso sect. It is renowned for its large, one-of-a-kind wooden stage, built without nails. From the stage, visitors can enjoy stunning views of the maple and cherry trees below.
Kiyomizudera Temple | Photo: Michelle Maria / Pixabay
Heading downhill towards Kodaiji Temple and Yasaka Shrine, you will pass the picturesque, historic streets of the Higashiyama district. The narrow streets of old-style wooden houses are lined with small handicraft shops, pottery sales, restaurants and cafés offering sweets and traditional tea.
If now is the time to look for a place to eat, you are in the right place. With a little luck, you might even find a tiny restaurant with sliding doors and low tables – and perhaps a trickling stream of water from a bamboo pipe.
Follow Ninenzaka down from the Kiyomizudera Temple | Photo: GD Quest / Pixabay
Kodaiji Temple, which dates from 1606, is located in the southern Higashiyama district. The first Tokugawa shogun, Tokugawa Ieyasu (1542-1616), provided the financial means for the construction. The interior of the main building was painted with lacquer and had lavish gold decorations. It is considered one of Japan’s finest cultural temple masterpieces. There is a pond garden and a temple garden of esthetic beauty. Moreover, the temple has a small bamboo grove.
The Gion Matsuri, the festival of Yasaka Shrine, takes place in July | Photo: Travel In Culture
You will continue to Yasaka Shrine, once called Gion Shrine, which dates back to 656. It is a characteristic landmark of Kyoto, especially the remarkable two-storey entrance gate is much photographed. The orange shrine also features a lovely garden with cherry trees, which makes the place very popular for hanami (flower viewing) during cherry blossoms in spring. As it is also traditionally a geisha location, there is even a chance that you might see a Kyoto geisha here. Especially during some of the festivals held at the shrine, you may have luck.
Evening at Yasaka Shrine | Photo: Michelle Maria / Pixabay
The Heian Shrine is a little further north. It is a long walk from Yasaka Shrine, but it is worth it! The shrine dates back to 1895 as a reconstruction of the former Heian Palace erected for the industrial exposition fair in Kyoto that year and dedicated to some of the emperors. It was built on the occasion of the 1100th anniversary of Kyoto’s foundation. After the exhibition, the copy was preserved, and it still holds significant religious and cultural significance in Japan today.
Walk all the way up to the impressive Heian Temple | Photo: Travel In Culture
Depending on your energy level, you can now take a walk around the Gion district. Alternatively, if, at this point, you have reached your limit of how many cultural impressions you can take in one day, you can postpone it to Day 2 as well! In Gion (and in the Pontocho district on the other side of the Kamo River), you can experience the true, authentic Kyoto atmosphere in the old streets with their original wooden houses. The Gion and Pontocho districts are the traditional geisha districts in Kyoto. Who knows, when they get lively in the evening, you might catch a glimpse of a kimono-clad woman – a geisha or perhaps the younger maiko (apprentice to a geisha)?
The Gion Matsuri festival in Kyoto | Photo: Travel In Culture
Depending on where you stay in Kyoto, you may also want to continue strolling in Northeast Kyoto through small alleys. Characteristic red lamps hang outside the restaurant fronts, guiding you to find a place to have dinner. Follow the small river that flows between low bamboo fences bordering gardens and homes and get a feel for the neighbourhood as it probably looked in the last hundreds of years. The streets are unexpectedly lush with plants along the river.
DAY 2: More Kyoto Temples & Shrines
The renowned Kinkakuji Temple is a must-see. If you want to use your Japan Rail Pass, you can take the local JR bus towards Takao from Kyoto Station. It has a route with a stop not too far from Kinkakuji Temple.
Kinkakuji Temple, or the Golden Pavilion, is the awe-inspiring, gilded pavilion, picturesquely located by a mirror pond with tiny islands and pine trees. It is one of the most famous temples in Japan. In 1397, it was built as a retirement pavilion for the shogun Ashikaga Yoshimitsu. That is probably the closest you will ever get to genuine beauty. The scenery is like an embellished painting. Follow the path around it to view the masterpiece of Japanese architecture from all possible angles.
Read more about Kinkakuji Temple – The Golden Pavilion in Kyoto.
Elegant, gold-plated Kinkakuji Temple | Photo: Travel In Culture
Within walking distance of Kinkakuji Temple, you’ll find Ryoanji Temple, a Zen temple from 1450. At Ryoanji Temple, you will be introduced to Zen Buddhism. The temple features the most famous Zen garden in Japan. It has the finest, seemingly polished pebbles, meticulously raked into the most decorative patterns. 15 rocks are laid out on patches of moss among the pebbles in a spectacular way. At no point can a visitor see all 15 stones simultaneously. At least one rock is always hidden, no matter what angle you look from. Try it out for yourself!
The idea of the rocks and the garden is not immediate. Several interpretations have been suggested. It is a place for meditation and deep thinking. Everyone is invited to come up with their interpretation beyond what has already been proposed: that the rocks are young, swimming tigers – or that they represent the concept of infinity!
The rock garden at Ryoanji Temple in Kyoto | Photo: Travel In Culture
After taking the bus (or some walking + a local train) back to Kyoto, you may want to have lunch before continuing sightseeing. Get off the bus or train near the historic Nijo Castle, which is next. There are quite a few restaurants south of Oshikoji dori.
Behind the famous Karamon main gate, the imposing stone walls and the beautiful gardens covering 275,000 square metres, you will find Ninomaru Palace, which has the most impressive rooms with lavish wall paintings. The complex of 6 buildings contains 33 rooms used for various purposes. The palace was the core of samurai society and the shogun’s residence from where he ruled. In addition to the residential rooms, there were waiting rooms for the feudal lords and for reception of the shogun’s audience.
The Ninomaru Palace, Nijo Castle | Photo: Travel In Culture
Passing through the most impressive palace rooms with tatami-matted floors and painted sliding doors, visitors are taken back to a bygone era. The nightingale floors of the castle were constructed in such a way that they especially creak in case of invading enemies. You should try the still-noticeable effect! The floors probably creak like birdsong when you step around!
The palace is surrounded by a rock garden of rare and scenic beauty, where rocks and trees flank a small pond. The rocks represent great authority, and the garden symbolises immortality.
It is now time to ‘gear down’ a little on temples and shrines and explore a famous market street. On your way back to central Kyoto, stop at the covered ancient shopping street Nishiki Market, where you can enjoy traditional Japanese food and pick up local souvenirs. It is a long street with small restaurants and food stands, with a variety of culinary delights, fresh seafood and other local specialities.
Nishiki Market | Photo: Travel In Culture
Afterwards, to experience the contrasts in shopping options, you can go to Kyoto Station and visit, for example, the Isetan store right next to the station. It is a large department store occupying 13 floors where you can find almost anything. If you still have room for a bite after Nishiki Market, your late afternoon snack (or dinner) can be delicious deep-fried seafood here – or a few pieces of delicate Japanese chocolate. In particular, there is a whole section devoted to chocolate, and it seems to be one of the busier departments. Delicious – and not cheap!
Traditional Kyoto street | Photo: Travel In Culture
If you hadn’t time to stroll around in the traditional Gion district on Day 1, you may wish to spend the evening in the Gion neighbourhood. Otherwise, head to the Pontocho district on the other river bank and take in the sights and atmosphere of the delightful, traditional Pontocho Alley between Sanjo and Shijo. Beware, some places don’t allow foreigners to enter! It is a real gem and one of the most scenic Kyoto streets.
DAY 3: Kyoto-Nara, Nara Temples, and Kyoto-Tokyo by Train
Trail of bright orange torii at the Fushimi Inari Shrine | Photo: Travel In Culture
Before the return trip Kyoto-Tokyo in the late afternoon/evening, spend the day in Nara. From year 710 until 784, Nara had the status of Japan’s first capital, and it still has eight historic temples and shrines, which today are UNESCO World Heritage Sites.
At Kyoto Station, take a few minutes to buy some food that you can eat later in Nara Park.
On your way out of Kyoto towards Nara, you might squeeze in the unique Fushimi Inari Shrine by first taking a local train to Inari Station, a short distance (5 minutes) from Kyoto Station. From Inari Station, it is only a few minutes on foot to the famous Shinto shrine.
If you have time, you can continue on foot through the overwhelming array of 10,000 orange torii and the 12,000 steps (or maybe you want to do only a part of the path!) up the mountains to the forest of the sacred Mount Inari. The trail is also part of the shrine grounds. Fushimi Inari Shrine is the most significant shrine and, at the same time, the headquarters of the 40,000 Japanese Shinto shrines honouring the god Inari. The bright orange torii portals in the forest are scenic – although they are even a little surreal!
Tokyo to Kyoto train – Kyoto Itinerary 3 Days
Then you jump on the train again bound for Nara, 45 minutes south of Kyoto. You can always check train departures on the website Japan Route Finder.
With its vast Nara Park and magnificent temples and shrines, Nara is a lovely place for day-trippers. Not surprisingly, it is a UNESCO World Heritage Site.
Nara: Todaiji Temple, with the Great Buddha Hall | Photo: Travel In Culture
The prestigious Todaiji Temple in Nara from the year 752 is a must-see. It is the landmark of Nara and the head temple of all provincial Buddhist temples in Japan. In its heyday, Nara was powerful and politically influential in shaping the government of Japan. As an attempt to reduce its power, the capital status was removed from Nara in 784.
The Great Buddha Hall is the largest wooden structure in the world and features this impressive 15 m high statue of the Cosmic Buddha (Daibutsu). It is truly enormous, and one cannot help but be deeply fascinated by the dimensions of both the Buddha sculpture and, not least, the hall itself!
Buddhist monks in front of Todaiji Temple in Nara | Photo: Travel In Culture
The impressive Kasuga Grand Shrine, Kasuga Taisha, is just outside Nara Park. The shrine was established at the same time as Nara and was dedicated to the god responsible for protecting the city. Kasuga Taisha is known for its many bronze lanterns, only lit twice a year, at festivals in April and in August. Smaller shrines can be explored in the forest around the main shrine.
Photo: Travel In Culture
The stunning Kofukuji Temple and its elegant pagoda are on your route. The temple was founded in 669 as the beginning of a larger temple complex around Kyoto, which eventually included 175 buildings. Today, only a few remain. The temple was moved from a suburb of Kyoto to Nara in 710 and is one of the most significant temples from the Nara and the Heian periods in Nara. It is a contribution to Buddhism in Japan and is one of the head temples of the Hosso sect. Kofukuji Temple has a five-storey pagoda, a three-storey pagoda and two octagonal buildings.
Enjoy a stroll around Nara Park, which was laid out in 1880. Both Kofukuji Temple and Todaiji Temple are inside the park itself. The park is also known as Nara Deer Park due to the significant number of deer that roam wild in the green areas. For the last hundreds of years, the deer have occupied the park. They are constantly protected, and penalties arise if you harm the animals.
If you have brought something to eat, Nara Park is the perfect place for a small picnic.
Over the years, the deer have learned to bow for snacks! However, there are signs warning visitors against close encounters! Nevertheless, most of the time, they seem to be calm and peaceful.
Tokyo to Kyoto by train – 3 Day Kyoto Itinerary
In the afternoon, catch the train back from Nara to Kyoto Station, in time for your Shinkansen train to Tokyo. If you can pick up your luggage near/at Kyoto Station, you’ll save time. You will now get a few hours of well-deserved rest on the Shinkansen train back to Tokyo! Perhaps grab a bento box at Kyoto Station for your train dinner!
For more information about the history of the temples and shrines in Kyoto, you may want to read 11 Must-See Temples and Shrines in Kyoto and Visit Kyoto Bamboo Forest and Snow Monkeys.
See our Tokyo Travel Guide for more helpful information for your trip to Japan.
If you have just 2 days in Tokyo, you may also want to read Best Things to Do in Tokyo – Itinerary 2 Days
Read next: Hotel with a Japanese Onsen in Tokyo
Tokyo to Kyoto by Train – 3 Days Kyoto Itinerary
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