The ultimate itinerary for a three-week backpacking trip to Japan!

Planning a holiday to Japan? In this blog, you will find the ultimate itinerary for three weeks of travelling and backpacking in Japan! In three weeks you will see the highlights of the country such as Tokyo, Kyoto, Hiroshima, the Japanese Alps and much more. Read on for a detailed travel itinerary for the ultimate trip to Japan!

Backpack in Japan: three fantastic weeks of travelling around Japan!

I think Japan is such a great country to travel in, however, making an itinerary for Japan I found quite difficult. There are so many special places and there is so much choice that sometimes I couldn’t see the forest for the trees. But now that I look back, our itinerary for Japan was really perfect. We had a fast pace, however, we had enough time to see everything we wanted to see. In addition, these three weeks gave a very complete picture of the different sides of Japan. But that does not take away, that I want to see so much more of Japan. With ease I could have travelled here for over two months, everything is so beautiful, impressive and completely different from each other.

That’s why I describe our itinerary below, but I also indicate which places we would definitely want to visit next time. Because there will definitely be a next time!

Route Japan: three-week trip by train in Japan!

Below you will find exactly our three-week itinerary in Japan. The itinerary is as follows:

Tokyo- Takayama (Japanese Alps) – Kyoto – Fukuoka – Hiroshima – Kumano Kodo Trek – Osaka

Map of itinerary Japan: Japan itinerary

Click here or on the image below to see our itinerary of 20 days in Japan. In this scheme, I also included our activities, the hotels where we slept, how much we paid for them and our travel hours.

What do these three weeks of backpacking through Japan look like?

Read on to see what exactly these three weeks of backpacking through Japan look like. You will also read about our personal experiences, including the hotel where we slept, and extra tips for Japan!

Itinerary three-weeks in Japan: 6 days in Tokyo

We arrive at 7:00 pm at Tokyo Narita and after another hour by train, we reach our apartment. The next six days we spend in this amazing city, Tokyo. Tokyo is immensely large and there is so much to see. The highlights for me are the fish market with fresh sushi, the Harajuku district, and the Shibuya Crossing, Japan’s busiest crossroads. But there is so much more to see and I really liked Tokyo. We do a day trip to Kamakura, a city by the sea with many temples.

Extra Japan tip: A trip that we did not make, but that seems to be beautiful when you love temples, is the environment of Nikko. In a wooded area, there is a large temple complex that is Unesco World Heritage. It only takes you 2 hours by train from Tokyo to get here.

I recommend you to stay at least 5 days in Tokyo, the city is really big and there is a lot to see.
In Tokyo, we stayed in an Airbnb and we paid € 61 per night for this!

Click here for our free Japan hotel guide!

Itinerary three weeks in Japan: two days in Takayama, the Japanese Alps

On the 7th day, we take the train to Takayama very early in the morning (+/- 4 hours). This is a city in the Gifu Prefecture, in the middle of the Japanese Alps. Here we stay for two nights in a traditional Ryokan, something I can recommend to everyone! The village is very cute to see and the perfect place for a little walk. The next day we rent a car (via Sunny Cars) and drive to Kamikochi, Unesco World Heritage. Here we make a beautiful hike through nature. Finally, we also visit the open-air museum Hida Minzoka, which shows what a traditional Japanese mountain village looked like several centuries ago.

Extra Japan tip: In two days you can see a lot of Takayama, but a few days longer let you have a more relaxed pace. When we would have had more time than we would go to Shirakawa-go or Gokayama where you can see many traditional farms.

We stayed in Takayama at the amazing Ryokan Oyado Yamakyu and paid € 137 per night for this. A lot of money but definitely worth it!

Itinerary three-weeks in Japan: three days in Kyoto

In 3 hours we travel by bullet train from Takayama to Kyoto, where we arrive around noon. Kyoto is known as the cultural city of Japan. There are many temples and other holy sites. The geisha is originally from Kyoto. There is also a lot of nature around the city.

We visit the district Arashiyama where there are many temples and where the famous bamboo forest is located. The latter is a bit disappointing. Kyoto is a city where many international and national tourists come and therefore it’s very busy in the city. This busyness and the weather that is not great makes us like Kyoto a little less than for example Tokyo. Although these two are of course impossible to compare with each other.

Other highlights of Kyoto were for me the Nishiki market, the red tori’s (arches) of Fushimi Inari Taisha and cycling through the city to the Golden Temple.

Extra Japan tip: 3.5 days Kyoto was enough for us to see everything in and around the city. However, we didn’t visit the town of Nara, which is known for the many deer who walk around here. If you want to go here, stay in Kyoto for at least 4 days.

We stayed in Cross Road Hotel, good but nothing special. This cost €63 per night.

Itinerary three-weeks travel in Japan: two days in Fukuoka

Fukuoka is the largest city on Kyushu, the most southern of the four main islands of Japan. It is a student city and because of its location on the coast, it seems to be wonderful in the summer. We travel from Kyoto in three hours to Fukuoka where we see the city by bike. This is very small compared to Tokyo or Kyoto, so in two days you can see everything. We also visit a Sumo wrestling contest and visit the Asahi beer brewery. Very nice to experience! I would like to go back again in the summer, in November this coastal town is a bit cold and grey.

Japan tip: If you have little time, I would consider skipping Fukuoka. You have to travel quite far to get here and there are no major attractions. It is useful to know, if you travel within Asia, it can be cheaper to fly to Fukuoka instead of the big airports in Tokyo or Osaka.

We stayed at the Tonagi Hotel, a fun backpackers which cost only €50 a night.

Curious what it costs to travel through Japan? Click here for our Japan budget blog!

Itinerary three-weeks in Japan: two days in Hiroshima

Hiroshima is a port city on the main island of Honshu. On August 6, 1945, this city was bombed by an atomic bomb. More than 145,000 people died and large parts of the city were completely blown away. The city is now completely rebuilt, but there is still a lot of attention for this sad event. There is an impressive Peace Park with the Peace Memorial Museum and the Atomic Bomb Dome.

We find this city very beautiful and impressive. Many Japanese people advise against going here, but we are glad we went anyway. Next time I would even take more than just two days for this city. The people are incredibly friendly, the city is beautiful and vibrant. A must near Hiroshima is the island of Miyajima. Here is one of the most famous Tori’s of Japan, the Itsukushima Shrine, and it is also a beautiful island to visit. There are deer around everywhere and you can hike to the top of the mountain. We take the cable car.

We stayed in Hiroshima at the hotel Park Side, a beautiful hotel on a perfect location. Price €46 a night.

Itinerary three-weeks backpacking in Japan: two days in hiking the Kumano Kodo trek

We leave Hiroshima early in the morning to travel to the prefecture Wakayama. In the summer you can surf in this entire region, so we definitely have to go back again. It’s also possible to stay in a temple in the city of Koyasan.

Now we are on our way to the beginning of the Kumano Kodo Nakahechi imperial route, a road that was walked hundreds of years ago by the pilgrims. We do a two-day tracking where we spend the night at local Ryokans. Beforehand it was quite a puzzle to find a suitable route and overnight stays. Here you can find the website that I have used to find information about the Kumano Kodo trek. You can also book the different Ryokans here. is not yet present in this area.

Our itinerary for the Kumano Kodo trek:

Before we start our tracking, we sleep in the town of Shirahama at the nice hostel Sandaya Guesthouse. The next morning we leave very early with bus 1 (here you will find the bus schedule) to the start of the hike in the town of Takijiri-oji. The first day we walk about 16 kilometres and sleep at the Ryokan Minshuku 3rd place in Chikatsuya Oji. The next day we walk 24 kilometres and arrive in Yunomine (near Hongu) where we sleep in the cosy hostel J-Hoppers Guesthouse. Here we enjoy the onsen (natural hot water baths) and the beautiful surroundings. We have our luggage transported for 15 euros from Shirahama to Yunomine.

Itinerary three-weeks in Japan: two days in Osaka

We spend most of our last days travelling. We are on our way to a hotel near Osaka airport since we will leave Japan very early in the morning the next day. After taking take bus 2 (here you can find the bus schedule) from Hongu to Tanabe, we take the train to Osaka. It is also possible to go by boat from Hongu to Tanabe, more information can be found here. Early in the evening, we arrive at our hotel. Early the next morning we fly to the Philippines.

I recommend that you stay in Osaka for two to three days so that you can see the city (and especially taste it)!

Free guide: all you need to know on the Japan Railway Pass (JR Pass)

Which highlights of Japan would we visit next time?

Oooh, we found Japan such a great country! On our way to the airport to leave Japan, we already fantasized about the next time. Then we want definitely want to visit the following places:


Hokkaido is the most northern island of Japan. Here you will find many mountains and in the winter lots and lots of snow. In the summer it can get pretty hot here and there are fields full of flowers. The capital Sapporo seems to be a nice, bustling city. In wintertime, the city has a big snow festival with large ice sculptures.

We would like to visit Hokkaido in the winter to ski here. Pricey? No not at all, apparently skiing is not more expensive than in the European Alps. In addition, with Japanese skiing, you end the day in an onsen (hot water baths), how cool is that!?

[Update November 2019: yes we booked a trip to Hokkaido! We will explore the island in April 2020!]


With a completely opposite goal, we would like to visit the southern Okinawa region: to relax on the tropical beaches. Okinawa consists of several tropical islands which, in terms of photos, are very reminiscent of the Philippines. Great place to end a holiday in Japan (we travelled to the Philippines after Japan so you understand that we didn’t visit this place this time).

Mount Fuji

Next time in Japan it is an absolute must for Ries to climb Mount Fuji. In this trip it wasn’t possible due to our timing: we were in Japan in November. Mount Fuji is open between July and the end of September. One of the most common climbs starts at station Kawaguchiko or Fuji-san. Keep in mind that you will need some extra days and be flexible when to visit it since the top is often unexpectedly covered in fog which will prevent you from climbing.

In the vicinity of Mount Fuji are also the five Fuji Lakes, beautiful lakes that I would like to visit.


This big city is known for its great food. Here we have to go next time, even if it is only for a day (and night), to experience the nightlife in the Minami district.


Naoshima is a small and very special island located between main island Honshu and the large island of Shikoku. The whole island is about art. There are several exhibitions, museums and large sculptures on the island. The best-known sculpture is the large pumpkin standing on a deck by the sea. You can reach Naoshima easiest by ferry from the city of Okayama on Honshu.

The island of Shikoku and the city of Kochi

The island of Shikoku can be reached in a very special way. You can cycle here from the main island of Honshu. There is a 60-kilometre long bridge between these two islands and it seems to be spectacular to bike over this bridge.

Once on the island of Shikoku, I would like to visit the city of Kochi. Next, to the famous Kochi castle, you will find beautiful long sandy beaches. Perfect during the summer.

Another place that I would like to visit Shikoku is the Iya Valley. This secluded spot is surrounded by steep mountains and rock faces. Across the valley are wooden walkways to get from one side to the other. You will also find many natural onsens here.

What highlights should you really not miss in Japan?

I find this a difficult question, there is so much in Japan that you really should not miss. Hereby my top five:

Highlight 1: You will have to visit Tokyo.
This city is vibrant and versatile. Culturally really indispensable in a trip to Japan, and it is the perfect place to start your visit to this country.

Highlight 2: Eat Sushi in Japan!
After the sushi in Japan, we are ruined for good … that is so good here. We ate fresh sushi at the fish market in Tokyo and did a sushi workshop.

Highlight 3: Definitely pay a visit to the cultural city of Kyoto.
Even though I prefer Tokyo, Kyoto shows you a completely different image of Japan. The temples here are beautiful!

Highlight 4: Hike a part of a pilgrimage (Kumano Kodo) and sleep in a Ryokan.
For me, our two-day Kumano Kodo trek really was the highlight of our trip. Nature is so beautiful and quiet. And in the evening you will sleep so tight on the big futons in a Ryokan. Unforgettable!

Highlight 5: Experience WO2 in Hiroshima.
One of the most impressive moments of our trip through Japan was our visit to the Peace Memorial Park. If you want to get to know Japan, this piece also belongs to me.

New friends in Japan, Tokyo

Have you visited a beautiful place in Japan that really should be included in this blog? Leave a comment!

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  1. by Martina Mizzi on 12 June 2020  14:54 Reply

    hi! thanks for the informative post :) looking to do the same trip, which jr passes did u get for this trip and what dates did u go in november as im looking to go in november also, thanks!

    • by Charlotte van de Sande on 13 June 2020  12:41 Reply

      Hi Martina,
      Such a cool perspective! We had the two week JR Pass, which was perfect for us! And we went from November 3rd until the end of November.

      Let us know when you have more questions!

  2. by Mackenzie Jervis on 5 January 2022  13:06 Reply

    This is a great itinerary that is really all-inclusive. It's hard to add any extra days to this itinerary but I would definitely advocate for Nara, and possibly Kobe from Kyoto as they're both great.

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