The ultimate 3 weeks in Japan itinerary

by suitcasestoriesbe
The ultimate 3 weeks in Japan itinerary

Planning to visit Japan? Here’s the ultimate 3 weeks in Japan itinerary including best places to stay, things to do and the best time to visit Japan.

Japan is the perfect blend between the newest technology, breathtaking nature, fascinating history and old traditions. That’s how we would describe Japan in only a few words. We traveled 3 weeks in Japan and visited incredible places like Tokyo, Mount Fuji, Takayama, Kyoto, Nara, and Osaka. Our Japan itinerary was literally a dream coming true!

We collected all the best tips and useful information in this 3 weeks in Japan itinerary. You’ll find a detailed travel itinerary of the route we did, the hotels & hostels we’ve stayed at, all the best things to do we highly recommend, our favorite places to eat, and tips on how to get around. And to make things easier, we put it on a map as well.

Tip: if you are traveling solo or would like to join an organized trip, definitely check the tours of Tourradar here. They have amazing adventure tours in Japan!

Our 3 weeks in Japan itinerary

START Tokyo | END Osaka

DURATION 19-21 days


BEST TIME TO VISIT JAPAN March-May (Spring, cherry blossoms) & October-November (Autumn)

WHEN DID WE GO October – November 2019

HIGHLIGHTS Tokyo, Kawaguchiko, Mount Fuji, Takayama, Kyoto, Nara, Osaka, Hiroshima

Japan in 3 weeks travel route + tips

Japan itinerary: Day 1-6: Tokyo

We flew with Singapore Airlines from Kuala Lumpur to Tokyo, where our trip of 3 weeks in Japan started. Tokyo is a destination on itself, where you can easily spend 1-2 weeks without getting bored. We absolutely love Tokyo and can’t wait to visit this amazing city someday again. From trendy neighborhoods, the cutest noodle shops and crazy robot shows to fascinating ancient temples. Tokyo has it all! Walk across the busy & famous Shibuya crossing, explore the streets in a real-life Mario Kart or shop in the world’s craziest electric town Akihabara. There are so many amazing things to do in Tokyo!

Tip: if you want to escape the crowds in Tokyo, go on a day trip to Nikko. Nikko has beautiful temples, hiking trails, and hot springs all surrounded by stunning nature. If you have a JR Pass, you can travel from Tokyo to Nikko for free and the journey will take around 1h 40 minutes. We didn’t get in Nikko ourselves, but it seems to be very beautiful.

Recommended stay

  • 4-6 days

Where to stay in Tokyo

As the world’s largest city it can be super overwhelming to decide where to stay in Tokyo. There are so many different areas in Tokyo and thousands of options for any budget. The best areas and places to stay in Tokyo which we personally like the most are Shinjuku, Ueno, Roppongi, and Asakusa. All these areas have a good connection with public transport and are located close to all highlights. A lot of shops and restaurants are also nearby. Perfect for anyone who’s visiting Tokyo for the first time!

Things to do in Tokyo

Where to eat vegan/vegetarian in Tokyo

  • We mostly went to the supermarket to grab lunch or get some vegetables for dinner. Our favorite supermarket to find healthy, vegan food was the Maruetsu Petit, which can be found in different places in Tokyo. For example, we paid JPY 796 ($7) for a salad bowl, bread, extra avocado + baked sweet potato
  • 8ablish Cafe near Shinjuku and Shibuya (healthy vegan food, beautiful interior, cozy atmosphere, be sure to book a table in advance)
  • Ain Soph. Ripple in Shinjuku (100% plant-based fast food restaurant, fav pick: the Ripple vegan burger with fries & vegan cheese)
  • Cococurry at the Omoide Yokocho or the Piss Alley in Shinjuku (they have vegetable curry rice plates which are quite good)
  • Falafel Brothers in Roppongi (our favorite place to grab a delicious falafel sandwich, only JPY 500 or $4)

How to get in Tokyo

  • Tokyo has two major international airports, Tokyo Narita and Tokyo Haneda. Tokyo Haneda Airport (HND) is the closest to the city center, only a 30-minute drive while Tokyo Narita Airport (NRT) is located 1-hour from the city but the most popular airport for international and direct flights. We flew from Kuala Lumpur with Singapore Airlines to Tokyo Haneda Airport and loved how quick and easy everything went upon arrival.

Check the best and cheapest flights to Tokyo here

  • From Haneda Airport, we took the late-night bus service (as we arrived at 01.00) to the city center (latest at 02.00 – 02.20) and paid JPY 1800 ($16) per person. The bus was super comfortable and we bought our ticket right at the counter when you exit the luggage hall. Check more information and schedules here. Taxis at night are super expensive (around $91) and trains are not running between 10 pm-5 am.
  • From Narita Airport, you can use the Narita Express train for free when you have a JR Pass. Trains run to Tokyo Station, Shinjuku and Yokohama every 30 minutes during most of the day and take about 53 minutes.  Check prices for the JR Pass or book it in advance here

Read also: How to get around Tokyo: our best tips for transport

Japan - Tokyo - Piss Alley or Memory Lane
Japan - Tokyo
Tokyo Shibuya
Tokyo streets Shinjuku

Japan itinerary: Day 6 – 8: Kawaguchiko (Mount Fuji)

On day 6, we went from Tokyo to Kawaguchiko which was definitely one of our most favorite places in Japan. In Kawaguchiko you’ll find the beautiful Kawaguchiko Lake which is the second largest lake surrounding Mount Fuji. The town itself is super small and has a lovely atmosphere. We loved renting a bike, driving around the lake, and finding some great spots to shoot Mount Fuji.

Recommended stay

  • 2-3

Where to stay in Kawaguchiko

Things to do in Kawaguchiko

  • Rent a bike and drive around Kawaguchiko town (JPY 1500/day or $14)
  • For stunning views of Mount Fuji, take the local train to Shimoyoshida and hike up the 400 steps to the Chureito Pagoda. Simply stunning! (15-minute walk from the train station)
  • Visit Oishi Park for a panoramic view of Lake Kawaguchi and Mt.Fuji (free entrance)
  • Relax and hang around Lake Kawaguchiko, which is one of the Fuji Five Lakes surrounding Mount Fuji
  • If you have enough time, drive with your bike to the Haha no Shirataki Waterfall (small hidden waterfall with a shrine)
  • Watch the sunset at the Ubuyagasaki Shrine where you see Mt.Fuji reflected in Kawaguchiko Lake
  • Another great sunset (or sunrise) spot is the walking trail near the northern shore of Lake Kawaguchiko where you also find the Museum of Art and Maple Corridor

Where to eat in Kawaguchiko

  • Finding healthy, plant-based food in Japan (especially outside the big cities) is hard, but the supermarkets are really great. We loved to cook our own meals at our hostel. Our favorite supermarket in Kawaguchiko was the Selva, inside of Bell Shopping Mall.

How to get in Kawaguchiko

  • We took the Highland Highway bus from Tokyo to Kawaguchiko (Fuji), which was a 2-hour journey. We booked our tickets in advance and paid JPY 2000 per person ($18) Super comfortable, relaxed, clean toilet on board and WiFi included. Highly recommended!
  • If you’re coming from Tokyo with the JR Pass, you need to switch trains at Otsuki, where you need to take the Fujikyu line to Kawaguchiko. This is a private line where you need to pay extra JPY 1440 per person.
Japen - Mount Fuji
Japan - Shimoyoshida - Mount Fuji street
The ultimate 3 weeks in Japan itinerary

Japan itinerary: Day 8 – 10: Takayama

On day 8, we went to Takayama a charming cute little town located in the foothills of the Japan Alps. The moment we entered Takayama, it felt like stepping back in time. Small traditional houses, some beautiful temples, shrines, a morning market, and peaceful parks where you have stunning views over the whole area. We enjoyed walking around the old town, visiting the Hida Folk Village, and watching the beautiful maple trees in Shiroyama Park.

Recommended stay

  • 2-3

Where to stay in Takayama

Things to do in Takayama

  • Stroll around the old town of Takayama where you find lots of museums, little vintage shops, and cute old traditional houses
  • Visit the old sake brewery and enjoy an authentic sake tasting
  • Rent a bike and visit Hida Folk Village, an open-air museum with 30 old farmhouses that illustrate the traditional way of life of the mountainous regions of Japan
  • Visit Shirakawa-go, a UNESCO World Heritage Site and one of Japan’s most picturesque places
  • Stroll around the morning market
  • Try Japanese archery in Hankyudojo (located in Takayama’s bar district, JPY 300 or $2,7 for 10 arrows)
  • Go to Kitayama Park with the sunset, there is a lovely bar called Ichi Bar where you can enjoy a coffee or glass of wine
  • Rent a car and drive to Kamikochi if you have more time (JPY 6500/full day incl insurance or $60)

Where to eat vegan/vegetarian in Takayama

  • Heianraku (wonderful local restaurant run by a lovely couple and known as the best vegan restaurant in whole Japan, serves both meat/vegan options, we took the 2-person combo set for JPY 3300 + the Gyoka dumplings. So so good! Be sure to book a table in advance, they only have a few tables inside)

How to get in Takayama

  • From Kawaguchiko we took the Nohi Highway Bus, which is the most recommended option and paid JPY 5000 per person ($46,5)
  • It’s also possible to travel with the JR Pass to Takayama, but you’ll need to transfer trains at different stations
Takayama during autumn
Japan - Takayama
Takayama old town
Japan route - Takayama

Japan itinerary: Day 10 – 15: Kyoto

We were very excited to visit Kyoto when we planned our trip to Japan and we quickly fell in love with it. Kyoto is also known as the cultural heart of Japan, as it was the imperial capital for over 1000 years. With 17 UNESCO World Heritage Sites, plenty of charming neighborhoods, historic castles, traditional houses, and many unique temples you’ll never get bored spending some more time in this magical city.

Kyoto is surrounded by mountains and inspiring places like the world-famous Bamboo forest or the thousands of orange Torri Gates at Fushimi Inari Shrine. And above all, it’s one of the few places where you still have the chance to see geishas at night.

Recommended stay

  • 4-6

Where to stay in Kyoto

Things to do in Kyoto

  • Wander through the iconic Arashiyama Bamboo Forest (go before 8 am to beat the crowds)
  • After a walk through Bamboo Forest take the Sagana Kanko Romantic Train, an old- fashioned steam train that takes you along some stunning nature sceneries (JPY 630 per person, not included in the JR Pass)
  • Hike through the thousands of orange Torii Gates at Fushimi-Inari Shrine (also here go as early as possible) or book this full-day tour.
  • Visit the Kinkaku-Ji Temple or also known as the Golden Pavilion with this half-day tour
  • If you like Japanese culture, go to Kyoto Imperial Palace
  • Get a matcha tea in a teahouse or join one of the authentic tea ceremonies
  • Walk around the Kennin-Ji Temple, the oldest Zen temple in Kyoto
  • Go for shopping to the lively Shijo-Dori Street(get off at Gion-shijo station)
  • Walk around the Nishiki Market, a local food market in central Kyoto
  • Visit the UNESCO world heritage site of Nijo Castle (JPY 1080 per person entrance fee, gardens only JPY 600)
  • Stroll around the beautiful Gion District in the late afternoon, where you’ll find lots of cozy restaurants, wooden houses, temples, and small alleys. This is also the place where you can take a glimpse of geishas if you’re lucky (mostly around 6 pm or later at night)
  • Another lovely place to walk around with sunset is Higashiyama District, another historic neighborhood in Kyoto

Where to eat vegan/vegetarian in Kyoto

  • Falafel Garden (perfect spot to grab lunch, vegan/vegetarian kitchen, our fav picks: falafel sandwich and hummus sandwich)
  • Choice Cafe & Restaurant (100% vegan restaurant)
  • AIN SOPH Journey (100% vegan restaurant in the heart of Kyoto, try their vegan burgers, curries or delicious desserts like the matcha pancakes)
  • Morpho Cafe (cute and cozy 100% vegan-friendly place, delicious vegan ramen, eggplant pizza, and other healthy treats)

How to get to Kyoto

  • We took the Kintetsu Highway Express Bus from Takayama to Kyoto and paid JPY 4500 per person, 4,5 hours drive
  • From Takayama, you can also use the JR Pass for the full journey, takes about 3 hours
  • If you’re coming from Tokyo, it’s only 2 hours and 40 minutes with the Hikari Shinkansen (included in the JR Pass)
Japan - Kyoto - Golden Pavillion
Japan - Kyoto - Bamboo Forest
Japan - Fushimi Inari Shrine in Kyoto

Japan itinerary: Day 15 – 16: Nara

Nara is a cute little town famous for its huge park where you can spot hundreds of free-roaming deer. There are special deer crackers for sale all around the park which makes feeding the deer the highlight. Most people visit Nara as a day trip from Kyoto or Osaka as it’only a short train away, but we loved staying here for one night and can’t recommend it enough.

Besides interacting with the lovely deers, there are some beautiful gardens, a five-storied pagoda, temples, and different shrines inside the park which are worth a visit too. In Nara town, you’ll find a few good bakeries and on the Higashimuki Shopping Street, you’ll find lots of souvenir shops and restaurants. 

Recommended stay

  • 1-2

Where to stay in Nara

Things to do in Nara

Where to eat in Nara

How to get to Nara

  • We took the Express Kintetsu Line from Kyoto to Nara and paid JPY 570 per person ($5). The journey is about 45-50 minutes. There is also a Limited Express train which has only 2 stops and takes only 35 minutes to get in Nara. (+JPY 520 yen per person more)
  • If you have the JR Pass you can also use the JR Line
Deer in Nara
Nara Park with sunset
Nara Park - mother and baby deer

Japan itinerary: Day 16 – 19: Osaka

Osaka is a foodie’s dream come true! Plenty of good restaurants, delicious street food and regional specialties like takoyaki (octopus balls) or Okonomiyaki (legendary savory pancakes). Osaka is known as the food capital of Japan and one of the best cities for foodies all over the world. So if you’re craving some good Japanese food we highly recommend adding Osaka on your Japan travel route. But besides the huge food scene, the city has many more amazing things to offer.

Photogenic streets filled with beautiful neon lights, cute little alleys to get lost in, lots of shopping districts, peaceful parks, and temples. One of our absolute highlights was Osaka Castle, which is one of the most famous landmarks in Japan and has a super fascinating history.

Recommended stay

  • 2-3

Where to stay in Osaka

Things to do in Osaka

Where to eat vegan/vegetarian in Osaka

  • Ali’s Kitchen (our favorite spot, great vegan/vegetarian options like hummus, falafel, curries and more, lovely owner too)
  • Organic & Vegetarian Cafe Atl (reasonably-priced set meals, lots of good vegan/vegetarian options)

How to get to Osaka

  • We took the train from Nara to Osaka, Express Kintetsu Line, and paid JPY 570 per person ($5,3)
  • From Nara, you can also use the JR Pass for the full journey, takes 30 minutes
  • If you’re coming from Kyoto, you can take the Shinkansen which is covered by the JR Pass and the journey takes only 12 minutes
Osaka Castle
Shinsekai Osaka Streets
Osaka Travel Guide - things to do in Osaka
Osaka Fish Market

Optional Japan itinerary: Day 19 – 21: Hiroshima

The last stop on our travel route for Japan in 3 weeks is the historic city Hiroshima. Hiroshima is worldwide known as it was destroyed by an atomic bomb during World War II in 1945. The city has recovered from the bombing and has now become a vibrant modern city with lots of great things to do. Unfortunately, we decided to skip visiting Hiroshima last-minute because we noticed that almost all highlights were in renovation for the Tokyo Olympics 2020. If we go back to Japan, we definitely add it again on our list.

Recommended stay

  • 1-2

Where to stay in Hiroshima

Things to do in Hiroshima

How to get to Hiroshima

  • From Osaka, you can use the JR Pass for the full journey, takes 1 hour 25 minutes

Plan your 3 weeks in Japan itinerary with our travel resources

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Felicidad Duskey March 24, 2020 - 6:07 am

The website is
one of the best we have found, and the Japan in 3 weeks: travel
route, guide + tips article is very well written and useful!

I want to share with you a link that also helped me a lot in cooking:
Thanks and kisses! 🙂

suitcasestoriesbe May 4, 2020 - 2:25 pm

Thank you so much for your sweet message! We are really happy to read that our Japan travel guide is useful. It means a lot to us!

Valerie & Mik


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