The Ultimate Two Weeks in Japan Itinerary: Where to Visit

For the first-timer, spending two weeks in Japan is the ultimate way to go. This Japan itinerary will break down exactly where to visit in Japan and how long to stay. Japan is a special place for me. After visiting for my third time this last year, it has become easily my number one destination in Asia.

Japan is wildly different from anything here in the U.S. Their culture has preserved the arts and historic components of society. Meanwhile, it has integrated technology and processes that drive their community forward. I’ve never seen anything quite like it — an incredible blend of the old world and the new world. Japan has a wonderful way of drawing you in and showing you a new way to live.

So if you’ve booked yourself a two-week trip to Japan, here’s everything you need to know about where to visit and why.

Why You Should Spend Two Weeks in Japan

How long you spend in Japan is entirely up to you. I would vote to do two weeks for a few reasons especially if it’s your first time. The first is that it allows you to get off the main path that most tourists will visit. All of those cities like Osaka, Kyoto, and Tokyo are wonderful. However, there are some other hidden gems of places to go. Spending two weeks gives you the right amount of time to truly digest it all. You can blend the perfect trip of highlighted cities and some other experiences that will take you by surprise. There are several world heritage sites you won’t want to miss as well along the way.

On our first trip to Japan, we booked in over two weeks and we felt we had really gotten a taste of the country. By the end of the trip, we were ready to go home. Our most recent trip was around 12 nights long and we felt we could have stayed the full two weeks. So my suggestion based on experience is that two weeks is the golden number.

What will be in this two-week itinerary in Japan post:

• A sample itinerary.
• Information on accommodations and dining.
• Sources for more detailed guides.
• What to Know About Transportation and the JR Rail Pass

Short on Time? Here’s How I Would Spend 2 Weeks in Japan:

Before Arrival

1. Purchase a JR Rail Pass, for unlimited train travel while in Japan

Stop 1: Tokyo — 3 nights

1. Shibuya Hotel En, for the best centrally-located hotel
2. Shibuya Granbell Hotel, for the best Shibuya Station hotel
3. Keio Plaza Hotel, for the best Shinjuku hotel

Stop 2: Kiso Valley — 2 nights

1. Magome Chaya, for the best Magome hotel
2. Ooedo Onsen Monogatari Hotel Kisoji, for the best hotel near Tsumago
3. Japanese Guesthouses, for the best intimate stays in the Kiso Valley

Stop 3: Kyoto — 4 nights

1. Kyoto Hotel Okura, for the best downtown hotel
2. Yuzuya Ryokan, for the best ryokan hotel
3. Hotel Mystays Kyoto Shijo, for the best budget hotel

Stop 4: Onsen Experience — 2 nights

1. Gora Kadan, for the best modern onsen hotel
2. Yaeikane, for the best traditional onsen hotel

Stop 5: Tokyo — 2 nights

1. Shibuya Granbell Hotel, for the best Shibuya Station hotel
2. Shibuya Hotel En, for the best centrally-located hotel

The Ultimate Two Weeks in Japan Itinerary

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Stop 1: Tokyo — 3 Nights

Tokyo Highlights

Starting in Tokyo is a wonderful immersion into Japan. I’d recommend flying into Narita Airport as it has a fast train into the heart of the city. Your first day or night will give you time to adjust to the changes. There are wonderful highlights to visit in Tokyo including incredible museums, neighborhoods, markets, and restaurants. You get an opportunity to experience Japan’s sprawling city.

A few favorites for me include spending a morning at Tsukiji Fish Market. It is certainly sensory overload but out of this world. One new thing we did this last trip was going to teamLab Borderless afterward since they’re both on the outskirts of town. It was a wonderful way to spend a day.

There are other day trips you can do as well like to the Fuji Five Lakes, so if you want a break from the city you can consider this. Overall starting your time in Tokyo is the most convenient for getting adjusted and from there you can continue on to your next destination with the extensive train routes.

Helpful Tokyo Guides to Plan Your Trip

• For creative things to do: The Alternative Guide to Tokyo
• Most recent coffee guide: A Guide to the Coolest Coffee Shops in Tokyo
• Back-up coffee guide: 7 Coffee Shops Not to Miss in Tokyo
• General travel guide: The First-Timer’s Guide to Tokyo

Where to Stay in Tokyo

I personally love to stay in Shibuya as it’s the best-located neighborhood to explore. A few recommended hotels:

1. Shibuya Hotel En, for the best centrally-located hotel
2. Shibuya Granbell Hotel, for the best Shibuya Station hotel
3. Keio Plaza Hotel, for the best Shinjuku hotel

Stop 2: Kiso Valley — 2 Nights

Kiso Valley Highlights

If there is one recommendation for getting out of the major cities, it’s to go visit the mystical Kiso Valley. It’s famed for the Nakasendo Trail where you can hike between the small towns of Tsumago and Magome. These two towns are historic and contain old-world buildings telling of Japan’s past.

Whether you’re looking to slow down, get some time in nature, or do something a bit more traditional like stay in a ryokan, the Kiso Valley is it. It does take some patience and time to plan this part of a trip to Japan as it’s only ryokans available in the towns. You can reach it by train from Tokyo with a few transfers and a final bus ride into Tsumago.

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Need A Japan Rail Pass? This Is Where I Book Mine

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Two nights is wonderful here and a welcomed reprieve from city life. This is mostly why I’d recommend doing it between Tokyo and Kyoto and you can easily follow the train routes.

Helpful Kiso Valley Guides to Plan Your Trip

• My personal experience: Visiting the Kiso Valley

Sample Train Route from Tokyo to Tsumago

You will need to bus from Nagiso to Tsumago, see schedule here

Where to Stay in Kiso Valley

I’d recommend staying in Tsumago or Magome which sit on either end of the Nakasendo Trail. Here are my top picks of where to stay in the Kiso Valley:

1. Magome Chaya, for the best Magome hotel
2. Ooedo Onsen Monogatari Hotel Kisoji, for the best hotel near Tsumago
3. Japanese Guesthouses, for the best intimate stays in the Kiso Valley

Stop 3: Kyoto — 4 Nights

Kyoto Highlights

Oh Kyoto, this city forever has my heart. Whether you come for the famed cherry blossom season that transforms the city or to explore the UNESCO World Heritage sites, it’s wonderful. Kyoto is a special place in Japan and a must on the first trip.

A few highlights for me are the Arashiyama bamboo grove in the early hours before the crowds. I’ve done it twice and each time it has been worth the early wake-up call to catch sunrise there. The red Torii gates of Fushimi Inari Shrine are another wonderful highlight as well. Fushimi Inari Taisha (full name) is not a world heritage site but nonetheless incredible.

You could easily spend 4 nights in Kyoto mostly because there is so much to do there. One way you can get out of the city is a day trip to Nara as well, utilizing the central train station. I’d recommend reading the extensive guides below to plan your days in Kyoto as there is a lot to do. That’s why I’d allot four nights in this city alone.

Helpful Kyoto Guides to Plan Your Trip

• Accommodation advice: Where to Stay in Kyoto By Neighborhood
• Temple and shrine guide: A Guide to the Best Temples & Shrines in Kyoto
• Local artisan shops: 7 Local Shops Not to Miss in Kyoto
• For photography: Best Photography Locations in Kyoto
• Where to eat: 20 Best Restaurants in Kyoto
• Where to get coffee: 7 Coffee Shops Not to Miss in Kyoto
• The overall guide: The Ultimate Guide to Kyoto

Sample Train Route from Tsumago to Kyoto

You will need to bus from Tsumago to Nagiso, see schedule here

Where to Stay in Kyoto

I have an entire post on where to stay in Kyoto and it is broken into the neighborhoods. The city is very diverse so I’d recommend giving it a read before making a choice on where you stay. The accommodation location in Kyoto makes a huge difference in your experience in the city.

Here’s my short list of best hotels in Kyoto:

1. Kyoto Hotel Okura, for the best downtown hotel
2. Yuzuya Ryokan, for the best ryokan hotel
3. Hotel Mystays Kyoto Shijo, for the best budget hotel

Stop 4: Onsen Experience — 2 Nights

Onsen Experience Highlights

A traditional experience in Japan is to go stay and enjoy the healing waters of an onsen. It’s truly Japanese in the sense of slowing down and restoring the body. After all the travel, I love to schedule this towards the end of the trip which is why I’ve placed it after four nights in Kyoto where you’ll walk a lot.

Since you’ll need to make your way back toward Tokyo eventually, you can choose a few locations. The more commonly visited area is Hakone which is filled with onsen ryokans. You can even get a day pass to the onsens and buy the Hakone Free Pass to visit the nearby sights. This is just one option if the area of Hakone is of interest.

We decided to spend a few more hours on a train and make our way towards the onsen region of the Yakushiyma mountains where the Yamashiro Onsen is. We splurged on two nights at Beniya Mukayu. It’s the single most expensive hotel we’ve paid for but in return received the best stay and a lot included. The hotel stay included daily breakfast and dinner, and our room had a private onsen. The food was exquisite, each meal several courses long with fine ingredients. Again this is a splurge experience but I’d say is well worth it.

You could choose to stay in this region (there are other onsen ryokans and hotels) as well. You’ll have to account for a few more transfers to get back to Tokyo but it is totally doable.

Helpful Onsen Guides to Plan Your Trip

• Our onsen experience: Staying at an Onsen in Japan’s Countryside

Sample Train Route from Kyoto to KagaOnsen

Local hotels pickup at the train station.

Where to Stay: Best Onsen Hotels

In Hakone, some of the top-rated onsen hotels include:

1. Gora Kadan, for the best modern onsen hotel
2. Yaeikane, for the best traditional onsen hotel
3. Hakone Airu, for the best Balinese onsen hotel

Check out 224 more hotel options in Hakone here.

For onsen hotels near the Beniya Mukayu in Kaga, see this page for the city of Kaga and over 40 options.

Stop 5: Tokyo — 2 Nights

Tokyo Highlights

We always tack on two more nights in Tokyo before leaving Japan. One reason is that we want to be in the city at least the night before our flight and the second is, there’s always something we didn’t get to. If you’re there for cherry blossom season, then definitely make an extra stop as the blooms could have changed.

I love eating once more at our favorite yakitori restaurant, strolling the gardens and shrines of Yoyogi Park, and soaking in the city’s energy. It’s a special city and one I always look forward to going back to.

Helpful Tokyo Guides to Plan Your Trip

• The Alternative Guide to Tokyo
• A Guide to the Coolest Coffee Shops in Tokyo
• 7 Coffee Shops Not to Miss in Tokyo
• The First-Timer’s Guide to Tokyo

Sample Train Route from KagaOnsen to Tokyo

Where to Stay in Tokyo

Before leaving Tokyo to go back to the airport, I’d recommend booking a hotel near the main train station like Shibuya for easy, direct access. Here are my top picks for best hotels when returning to Tokyo:

1. Shibuya Granbell Hotel, for the best Shibuya Station hotel
2. Shibuya Hotel En, for the best centrally-located hotel
3. Keio Plaza Hotel, for the best Shinjuku hotel

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Planning for Transportation in Japan

One of the most overwhelming parts of Japan is sorting out whether or not you need a Japan Rail Pass and the train systems. The rail pass and Japan Rail are incredibly easy to use and convenient pending a few factors. I have an entire blog post dedicated to transportation in Japan which goes into great detail on all of the factors to consider.

In short:

The JR Rail Pass is essentially a joint pass for the majority of the JR Company trains in Japan. Passes are available by either a 7, 14, or 21-day period. If you do a quick tally of individual ticket prices (especially between Tokyo, Osaka, Kyoto, and other regions) it will be worth it. You can use it on the JR lines in Tokyo and Kyoto which connect you between neighborhoods. You can purchase it through this link and it must be done so before arrival (give a few weeks to receive the pass). One other benefit is the ability to reserve seats on certain trains.

*You’ll find each train station easy to navigate and the famed bullet train really is wonderful. Trains in Japan are timely so be prepared to arrive ahead of time.

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Other Destinations to Consider for Your Two-Week Japan Itinerary

There are several other destinations you can consider as even Hakone mentioned above. One popular other destination is Hiroshima which is home to the Hiroshima Peace Memorial and Peace Memorial Park. I know so many people love to visit as the Peace Memorial Museum is incredibly special. A few other destinations to consider are:

• The Alpine Route
• Miyajima Island
• Osaka (wonderful for a few days in a different city)
• Takayama

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