3 Week Japan Itinerary

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Planning a trip to Japan? Let’s dive in to my three week Japan itinerary!

I know it sounds crazy, but I was never super interested in traveling in Japan, at least compared to other countries on my bucket list. Well my 3 week trip to Japan completely changed that. I absolutely fell in love with Japan – from the bustling streets of Tokyo and tea houses of Kyoto to the hiking trails of Nagano and Kamikochi. Japan quickly became one of my favorite places that I’ve ever visited.

This article will cover our exact itinerary for the three weeks we spent in Japan, plus some additional tips to help you plan the perfect trip. I’ll be diving into all of the details including our Japan itinerary route, where we stayed, where we ate, and more!

Before we dive into the article, here are some popular tours in Japan to book if you are in a rush:

Places to visit: 3 Week Japan Itinerary

Here are all of the places that we visited on our 3 week Japan trip, including a few day trips.

• Nagano
• Matsumoto
• Kamikochi (day trip)
• Takayama
• Kanazawa
• Tokyo
• Kyoto
• Uji (day trip)
• Nara (day trip)
• Osaka

How to get there

Before we dive into my 3 week Japan itinerary, it’s important to discuss how to get to Japan in the first place. You can find direct flights from US destinations to Japan from major airports like JFK, LAX, SFO and SEA. From NYC to Tokyo it is a direct 15 hour flight, while a flight from LAX is only 10 hours.

Most flights from the US arrive into Tokyo, unless you have a layover somewhere else in Asia enroute. In Tokyo there are two major airports – Narita (NRT) and Haneda (HND). If you have the option to fly into Haneda airport, I recommend it. Unlike Narita, which is about 1.5 hours from the city center, Haneda is only about 40 minutes. It is a quicker and cheaper journey into the city center by both taxi and public transportation.

Things to know before visiting Japan

Japanese culture is super unique and differs quite a bit from US culture. While some cultural norms are pretty straight forward, here are a few things to know before embarking on your 3 week Japan itinerary.

• 1) Taking off your shoes: Taking off your shoes is common practice in Japan. You should expect to take off your shoes when entering any households or dining in a restaurant. There are also some shops that require it, so look out for signs.
• 2) Expect people to not speak English: While travelers should never assume that locals will speak English, far less locals speak English than other Asian countries. Many restaurants only have menus in Japanese characters, so downloading an offline Japanese to English translator will be your best friend.
• 3) Getting a Suica card is a must! These can be used for metro rides in Tokyo, at konbinis (7/11 and Family Mart), and even at vending machines. You can download this onto your phone and reload virtually in your wallet.
• 4) Food is cheaper than you think! Yes, you can splurge on super fancy and expensive meals. But there are so many places to eat AMAZING ramen, sushi, etc on a budget.
• 5) A lot of places are cash only, and many ATMs have a minimum withdrawal amount. Plan accordingly!
• 6) Tipping is not a standard practice in Japan.
• 7) In order to get a tax refund when shopping (which you want to do to save money), you will need to have your passport on you. A copy of your passport won’t work.

Day 1-2 Nagano

Day 1: Narita International Airport (NRT) to Nagano 

We kicked off our trip in Nagano, a mountain town in central Japan. Nagano is located about 1.5 hours by train from Tokyo Main Station, accessible via a direct train on the JR Line. We started our journey at the Narita Airport, where we took a train to the Tokyo Main Station, grabbed a quick dinner at the train, and continued on our way on the Shinkansen, Japan’s bullet train. 

If you are picking up a JR Pass, you can use it for this entire journey. Otherwise, there are cheaper alternatives, such as the Keisei Line. 

Although our trip to Japan was three weeks long, we only got a 2 week JR Pass, as we planned to be relatively stationary during the final week. With the recent increase in train prices, I recommend pricing out all of your routes to decide if a JR Pass makes sense for you. In most cases, it probably doesn’t.

Once you arrive in Nagano, there are a number of local trains and buses to reach your final destination. 

Lodging: DOT Hostel 

Day 2: Nagano and the Five Shrines of Togakushi 

Today is our first official day in Japan, since we arrived in Nagano late the night before. We started our morning with a matcha from MACCHA HOUSE and a stroll through the beautiful Zenkoji temple before hopping on a bus into the mountains to hike the five shrines.

If you’re planning a trip to Nagano,, I highly recommend a day trip to hike the trail of the Five Shrines of Togakushi. Located 1 hour from Nagano, Japan, the shrine area is the perfect place for enjoying Japan’s trails. It is absolutely stunning in any season.

Buses depart from either the main station in Nagano or by Zenkōji Temple, and take around 1 hour. There are multiple bus stops by the various shrines. You can walk between all 5 shrines, as we did, or simply get dropped at the one you plan to visit. We started at the Togakushi Hokosha and finished by the path to Togakushi Okusha.

If you are choosing between the upper and lower shrine area, I highly recommend the upper shrines. It is believed that the path to the upper shrines is lined with trees that are over 900 years old!!

Make sure to grab fresh soba noodles before or after your hike right next to the Togakushi Hokosha stop. Restaurant is 戸隠･手打ちそば つる家 on Google Maps. The staff here don’t speak English (nor should you expect them too), so make sure to have Google Translate downloaded and Japanese saved in offline mode.

Back in the city, there are tons of delicious dining options as well. I recommend checking out Ramen Misoya or Nagano Meijitei. 

Lodging: DOT Hostel 

Day 3-5 Matsumoto

Day 3: Nagano to Matsumoto 

We had a slow morning in Nagano before hopping on a short train ride to Matsumoto. The train runs along the JR Line and takes around 1 hour. There are a ton of great restaurants near the train station in Nagano, or you can stop at the konbini (Japanese convenience store) to pick up food for the ride.

I absolutely loved Matsumoto! The city is set cradled between the mountains, with tons of great restaurants and charming streets. 

We stayed in a hostel dorm (which I was a bit hesitant to do at this point in my life) but it was so lovely. The hostel was beautiful, quiet and clean. It was just a short walk to the city center, making it the perfect base.

For dinner we had the delicious ramen from Mansho Sakura. They don’t take reservations but the line moves quickly. It’s definitely worth it.

Day 4: Matsumoto 

We started our day at the beautiful Matsumoto castle (with a matcha in hand of course). I recommend taking your time enjoying the castle and its property. We also came back at sunset because it was just so gorgeous.

I had a low-key day since I was letting my sprained ankle heal a bit (oops). But I recommend renting an e-bike and biking to the nearby wasabi farm where you can try the famous wasabi soft-serve ice cream.

In the town, make sure to check the adorable Nawate shopping street. There is a cute cafe at the end of the street called Storehouse Cafe & Bar for a little matcha treat.

For dinner, make sure you make a reservation ahead of time at Yamameya, a delicious Izakaya. Afterwards, we grabbed a few more small bites and sake from Ikaruga-no-sato. Their sake selection is incredible.

Lodging: ゲストハウスまたたび

Day 5: Matsumoto and Tsumago

For our final day in Matsumoto we took a day trip to Tsumago, a post town on the Nakasendo route between Kyoto and Edo. It is known today as being one of the best-preserved towns showing the traditional style of the Edo-period.

You can take a train+bus combo to Magome-juku. From here it is a stunning 2 hour walk to Tsumago.

While in Tsumago, here are a few spots to check out:

• Kojitsu Coffee (Good Day Coffee & Bar) – for a little coffee or matcha treat
• Rikyu – for delicious soba noodles
• Soft serve ice cream – served at a number of shops along the main road

Lodging: ゲストハウスまたたび

Day 6-7 Takayama (via Kamikochi)

Day 6: Kamikochi and Takayama

This was easily one of my favorite days of our three weeks in Japan. There are options to take a bus directly between Matsumoto and Takayama, but we decided to take a detour and spend the day in Kamikochi. Kamikochi is one of the most beautiful parks in Japan, offering endless hiking trails and camping opportunities. If you have the time and it is the right time of year then I recommend camping or spending a night in an overnight hut. If not, you can simply do what we did instead!

There are only a limited number of buses between Matsumoto and Kamikochi each day, so our only option was to take the 5:30am direct bus from the main station. It’s an early morning, but well worth it to arrive at the park by 7am before the main crowds. If you are planning to visit Kamikochi, especially as a day trip, then I definitely recommend taking the early bus because the park gets super busy.

This bus is not on the JR Pass as it is operated by a private company, Alpico Kotsu Co, purchased on Japan Bus Online. 

Kamikochi park is open from mid-April to mid-November. There is no cost to enter the park itself, but if you are visiting as a day hiker you can store your luggage for a small fee.

Getting to Takayama

Just down the road from Kamikochi, you can visit the onsen at Hirayu no Mori. There is a bus from the park to the onsen, and direct buses to Takayama just beside the onsen. It’s an amazing place to relax after a long day of hiking. Entrance to the public baths cost around $7 USD (as of November 2023) and are separated by gender with both indoor and outdoor tubs available. It is tradition to enjoy some flavored milk after your soak, but the milk-flavored soft cream is a great alternative as well!

I highly recommend making dinner reservations in advance. Takayama is not a particularly large place so dining options are limited. Our first night we were turned away from so many restaurants before finding a spot to eat at the delicious Akariya, known for their Hida Beef. We learned our lesson and made a reservation for the following evening and had no problems!

Lodging: K’s House Takayama Oasis [2nd K’s Hostel]

Day 7: Takayama 

I really loved Takayama, the “Little Kyoto” nestled in the Japanese Alps. Takayama is often overlooked by tourists more keen to visit the popular cities of Tokyo and Kyoto. It’s not a place that you need to spend a ton a time in, so even if you just have one full day you should be good.

We started our morning in in the charming historic Old Town (Sanmachi Suji District) with matcha at Cha-no-me cafe, before jumping in line to to try the famous Hida beef sushi from Hida Kotte Ushi. I personally didn’t try it, but Jon loved it!

From here you can make your way to the Miyagawa Morning Markets. This is a great market along the water for trying local dishes and buying small souvenirs.

We took our time in Takayama, simply strolling, journaling and taking photos, rather than rushing around to popular spots. Some popular things to do though are a visit to a local onsen and the nearby Shirakawa.

In the evening we popped back over to the Old Town for some sake tasting at the local sake breweries before our reservation at Tenaga Ashinaga for some incredible ramen.

Lodging: K’s House Takayama Oasis [2nd K’s Hostel]

Day 8-9 Kanazawa

Day 8: Takayama to Kanazawa 

We woke up and had just enough time to grab a matcha (always), stop in a few shops and enjoy a 7-11 breakfast before heading to the train.

We had a private room at K’s House Takayama Oasis [2nd K’s Hostel], which we loved because it was just a 5 minute walk to the train station.

Our next stop was to the lovely city of Kanazawa. I loved Kanazawa because it is a big city, but with far less crowds than the more famous cities of Tokyo and Kyoto.

We didn’t make any reservations ahead of time (oops) but we were able to grab a seat at Uguisu ramen. A small ramen shop serving up delicious bowls of hot ramen.

After dinner we had the chance to visit the Team Labs pop-up location at the Kanazawa Castle. While this likely won’t be available during your visit (limited time only), I’d check where else they currently are. It’s a fun alternative to the Tokyo Team Labs, which is expensive and often sold out.

Lodging: Airbnb 

Day 9: Kanazawa 

What better way to start the day then a stroll through one of the most beautiful gardens in the world AND a matcha soft serve ice cream for breakfast? I really don’t think that it gets better than this!

Kenrokuen Gardens is a must on any Kanazawa itinerary. You could easily spend hours here walking around and hanging out. I recommend visiting early because it gets quite busy. After, I treated myself to one of the best matcha ice creams that I had in Japan from Sawawa Japanese Maccha Sweets. I dream about this matcha soft serve daily.

Now it’s time for lunch!

If you’ve been to japan that you already know that waiting in line is simply a thing that you do. BUT there are ways to avoid a long waiting time.

If you’re visiting Kanazawa, Japan you need to eat at Mori Mori Sushi in Omicho market. The restaurant opens at 8am so you could stop by for some breakfast sushi. Otherwise, arrive before the lunch rush and put your name on the list. Then you’re free to roam around a explore the market while you wait.

We spent 7,000 yen for 2 ($46 for 2) for a huge plate stack of sushi

Lodging: Airbnb 

Day 10-14 Tokyo

Day 10: Kanazawa to Tokyo

One final stroll through the charming streets of Kanazawa and we were off to Tokyo! The train ride takes about 4 hours, so it’s a decently long journey door to door.

Which means our first stop in Tokyo could only be one time… more matcha! I grabbed a delicious matcha latte from The Matcha Tokyo. We made our way through the famous Shibuya Crossing before grabbing our first meal in Tokyo – Uogashi Nihon-Ichi Shibuya Dogenzaka – Standing Sushi. I could eat here everyday of my life.

We had time for a little shopping (check out Hands and Loft), before heading to our reservation at The Sake Market. 90 minutes of unlimited sake. It’s such a fun experience and a great way to try tons of different sakes. And you can bet that lots of games were played post unlimited sake.

Lodging: Comfort Inn Roppongi

Day 11: Tokyo

What better way to cure a sake hangover then with sushi for breakfast? We made our way to Nemura Hanamaru (I recommend arriving before they open) to enjoy some delicious conveyor belt sushi. And if that wasn’t enough, we followed it right up with some spicy noodles from Ginza Rosokuya.

More shopping was in order today. Japan truly has some of the best shopping in the world. I grossly overestimated how much I could fit in my backpack but somehow we made it work.

I’ll admit that we went to Ichiran for dinner. I know it’s a chain. I know it exists in NY, trust me I’ve been many times. But I still love it! We followed up dinner with mango kakigori from yelo. A must-try dessert in Roppongi.

Lodging: Comfort Inn Roppongi

Day 12: Tokyo

We started our next morning in Tokyo early strolling through the streets of Asakusa. This is a great place to check out a number of traditional temples, and try various Japanese street foods. We enjoyed everything from creme-filled melopan and matcha ice cream (always) to fried pork bites and mitarashi dango.

There is a great lunch spot in the area that does fresh onigiri (Onigiri Asakusa Yadoroku). This is also where you’ll find the famous “strongest matcha ice cream” from Suzukien Asakusa. Unfortunately it was closed during our visit. So please enjoy some for me!

In the evening we made our way to Shimokitazawa, Tokyo’s boho area. I wish we had spent more time here, the thrift shops are amazing!

But we did manage to grab some yummy noodles and enjoy a few local bars (I even found amazing natural wine here at Wine Laundry). We bought tickets to a local jam sesh at BASEMENTBAR. This is a great way to enjoy local music for cheap, and immerse yourself in the local nightlife a bit.

And what better way to soak up the drinks then a midnight Udon noodle session at the delicious TsuruTonTan. Such a perfect late night (aka middle of the night) meal!

Lodging: Comfort Inn Roppongi

Day 13: Tokyo

Another day in Tokyo, another day enjoying my morning sesame bun from 7/11 before spending the rest of the day eating. It was a bit of a trek to today’s ramen spot, but it was super worth it! Make sure to add a stop at Karashibi Miso Ramen Kikanbo to your list.

Since we decided to skip some of the bigger attractions like the Tokyo Tower or Team Labs, much of our day is spent walking 30,000+ steps simply enjoying the energy of the city.

For dinner we grabbed a spot in line at Tonkatsu Hinata, just north of Shibuya, for some of the best pork tonkatsu of my life. It’s definitely worth a visit. And while you’re in the area, make sure to check out a jam sesh at the Jazz Spot Intro. Entry costs around $6 USD (as of 2023) and includes one free drink. It was such a great way to end our time in Tokyo.

Lodging: Comfort Inn Roppongi

Day 14-19 Kyoto 

Since we are traveling full time and needed to factor in at least one full work day, we gave ourselves 5 full days to explore Kyoto. Because I was working quite a bit while in Kyoto, I’m going to share an overview rather than a day by day breakdown.

If you’re planning it into a normal vacation itinerary I’d recommend 3-4 days. This is enough time to take a few day trips and explore Kyoto itself. Since Kyoto isn’t huge, you can probably cover most of the main attractions in about a day and a half. 

Here are my must-visit places in Kyoto:

• Kiyomizu-dera
• Nanzen-ji Temple
• Fushimi Inari Taisha
• Rengeō-in temple
• Kinkaku-ji
• Ryōan-ji
• Philosophers Path
• Eikandō Temple
• Higashiyama Jisho-ji
• Heian Shrine

I would start one morning at Fushimi Inari Taisha, followed by Rengeō-in temple, and one morning at Kinkaku-ji followed by Ryōan-ji. Kiyomizu-dera is best visited at sunset, when you can see the colors changing over the city. 

Other than Kinkaku-ji and Ryōan-ji, which are located in the Northwest section of the city, most of Kyoto’s attractions can easily be visited by bike. Just make sure to look up bike specific parking lots, where you can pay a small fee to lock up your bike.

If you want all of the details for your time in Kyoto, you can check out my Kyoto travel guide.

Where to eat in Kyoto

• Katsukura Tonkatsu 
• Tai sushi 
• Ichiran 
• Mimikou 
• MACCHA HOUSE 

Feel like getting more hands on? You can even book a class to learn to make your own ramen or Japanese bento box.

Lodging: Airbnb (unfortunately it is no longer available)

Day trips from Kyoto, Japan

We took day trips to four spots outside of Kyoto, all of which I highly recommend. It’s a great way to see more of the country while having a base – and to avoid the crowds.

Let’s dive into each of these trips in a bit more detail:

Uji 

If you’re looking for a perfect half day trip from Kyoto, Uji,  the historic home of matcha tea, is the perfect destination. If you know me then you know that I love matcha. I’ve drank it almost every morning for over 5 years. So of course I jumped at the chance to visit a beautiful city only 30 minutes from Kyoto that specializes in matcha.

We signed up for a matcha making class at Fukujuen Uji. This is a great place to learn about and interact with matcha. We booked the “making matcha with a stone mill” experience. The experience takes about 45 minutes and costs 1,650 yen (~$11 USD).

To get to Uji from Kyoto you can take either the JR line or Keihan line directly to Uji. The train ride is only about 30 minutes. It is located halfway between Kyoto and Nara, so we actually combined the two into a full day adventure.

Nara

We arrived in Nara from Uji and did a combo day trip to both in one day from Kyoto. It’s great day trip on it’s own as well, with the famous deer and tons of incredible temples.

How to get to Nara

You can reach Nara from Kyoto in just 45 minutes. There is a rapid train on the JR line covering this route. If you do not have a JR pass, you can also take the Nara Line and transfer to the Keihan Line. This may make more sense depending on where in the city you are staying.

Things to do in Nara

• Feed (and bow to) the deer of Nara
• Try the famous mochi at Nakatanidou
• Grab lunch at Kasuya Nara Sanjo
• Visit Kofuku-ji, a famous Buddhist temple
• Enjoy the Kasuga Taisha

Mt. Kurama

I’m truly shocked that more people aren’t talking about this beautiful shrine area. Mt Kurama is a mountain and shrine area located just a short 25 min train ride north of Kyoto, and yet we only saw a handful of other tourists when we visited. 

Mount Kurama is considered a sacred mountain with great spiritual significance, especially in Japanese folklore and religious traditions.

You can hike along a mountain pass and visit a number of beautiful shrines along the way. It’s the perfect half day 2 hour hike from Kyoto. The majority of the path is well maintained with stone steps.

The main attraction is Kurama-dera Temple, which is located near the top of the mountain, offering incredible views. 

To shorten the hike, you have the option to take a cable car part of the way up the mountain. If you are looking for a more relaxing experience, there a many traditional onsen baths in the area of Mt Kurama.

Ohara

 Just a short 35 min bus ride from Kyoto and you’ll be in the charming town of Ohara. You’ll find tons of restaurants and shops, and the beautiful Sanzen-in Temple. If you enjoy hiking, there are beautiful trails from here that lead all the way to Mt Kurama shrine trails

Just take bus 17 all the way to Ohara. It should be around 700 yen ($4.60 in November 2023).

I highly recommend enjoying a matcha ceremony at the Sanzen-in Temple. There is no need to reserve one ahead of time. The matcha ceremony is 600 yen ($3.95 as of November 2023) per person

Day 20-21 Osaka

Our final two days in Japan were spent in Osaka. I’ll be honest, I didn’t love Osaka BUT we were also staying right downtown in a super touristy area so I think that played a big roll in it.

Most of the places that we ate were just fine. The highlight was definitely Ajinoya – typically Okonomiyaki. The lines are always crazy, but it’s totally worth it! One of my favorite things that we ate during our three week Japan itinerary.

Another highlight was visiting the Tsutenkaku Tower and checking out all of the fun retro games in the area.

Visiting Japan? Here are some other articles to check out:

• 21 Best Things to do in Kyoto, Japan
• Best Things to do in Takayama, Japan
• Uji, Japan: Everything you need to know
• 12 Beautiful Places to Visit in Japan

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