An active and eclectic 12-day Japan itinerary featuring the Tokyo metropolis, the Snow Monkeys in the Japanese Alps, a scenic hike on the historic Nakasendo Road, the ancient capital Kyoto, and the art island Naoshima.

Our sample Japan itineraries are here to inspire you. They are not fixed itineraries, and can be customized or altered in almost any way.

Learn more about trip planning with Boutique Japan.

12 daysApprox. US $900 per person per day (read more about pricing)Based on your preferred travel dates

Trip Highlights

  • A tailor-made itinerary crafted personally for you, based on our in-depth Japan expertise, relationships, and firsthand experience
  • Tokyo, one of the world’s most exciting cities
  • Historic Nagano and the Snow Monkeys in the Japan Alps
  • The Nakasendo Way and the picture-perfect village of Tsumago in the rural Kiso Valley
  • Kyoto, the heart and soul of traditional Japan
  • Stunning art and architecture on Naoshima, including a stay at Benesse House
  • All your accommodations, in hotels and ryokans to match your taste and priorities
  • Private, non-touristy tours with fun and knowledgeable local expert guides
  • Seamless logistics and in-country transport via the shinkansen (bullet train) and more
  • Extensive pre-departure information to help you prepare for your trip
  • A Japan specialist to answer your questions, and thoughtful customer service
  • And more!

Vermillion torii gates of Fushimi Inari Taisha Shrine in Kyoto, Japan

Itinerary Details

Plenty of great travel companies offer active trips featuring highlights of both urban and rural Japan. What makes our itineraries unique?

We live and breathe Japan (learn more about us), and our exceptionally personalized trip-planning process ensures you’ll have a truly one-of-a-kind, immersive trip.

Most importantly, even in well-known places like Tokyo and Kyoto — and increasingly popular destinations such as Naoshima, the Japanese Alps, and the Nakasendo — our specialty is helping travelers have highly authentic, non-touristy experiences.

So let’s dive in!

Day 1: Arrive in Tokyo, Japan

On arrival in Tokyo, you’ll be met and transferred by private vehicle to your lovely accommodations. Settle in, adjust to your exciting new surroundings, and get ready for your adventure ahead!

You can fly into either of Tokyo’s two major airports, Narita (NRT) or Haneda (HND). This sample itinerary can also be customized to begin in the Kansai region (where Kyoto and Osaka are located), flying into either of Osaka’s two major airports, Kansai (KIX) or Itami (ITM).

Your Tokyo hotel: Palace Hotel Tokyo or Conrad Tokyo

Skyline of the Shinjuku district in Tokyo, Japan

Day 2: Modern Tokyo Highlights & Evening Whisky Tasting

Ohayou gozaimasu (good morning)!

Today is your first full day to begin taking in the Tokyo metropolis. You’ll begin with an immersive half-day tour introducing you to the city, and end with a memorable Japanese whisky tasting.

After a delicious breakfast at your hotel, you’ll be met by your insightful private guide. While Tokyo can certainly be enjoyed without a guide, exploring with a fun and knowledgeable expert by your side will dramatically enhance your experience.

At Boutique Japan, we have exceedingly high standards when it comes to private guides, and carefully design each private tour to cater to your unique priorities and interests.

Tokyo is one of the world’s liveliest cities, full of amazing restaurants, beautiful gardens, stunning modern architecture, charming backstreets, and a glittering neon-filled cityscape. Beyond the city lights and crowds, Tokyo is also full of quiet neighborhoods where you’ll find locals going about their daily lives, and countless hidden gems in the form of unsung yet wonderful little shops and restaurants.

Explore unique neighborhoods such as (for example) Naka-Meguro, Yanaka, Aoyama, Omotesando, and Asakusa; along with one or more excellent museums, shrines, or gardens such as the Tokyo National Museum, Meiji Jingu Shrine, and Shinjuku Gyoen National Garden (explore more of our favorite Tokyo neighborhoods).

Following your fascinating tour, you’ll have some time to relax at your hotel and recover from any remaining jet lag you may have, or continue exploring independently. For your free time, you’ll be able to take advantage of the pre-departure materials we provide to each of our travelers.

This evening you’ll venture out on an immersive Japanese whisky tour. Japanese whisky is world-renowned for good reason, and there are few better places to drink it than in Tokyo, which is home to some of the best whisky bars on the planet. As part of your outing you’ll visit a couple of different bars, where you’ll have the chance to sample a variety of excellent Japanese whiskies.

Meiji Jingu shrine in the Harajuku neighborhood of Tokyo

Day 3: Backstreets Cycling Tour of Tokyo

Most first-time visitors envision Tokyo as an ultra-dense, crowded metropolis. While it’s certainly true that some of Tokyo’s neighborhoods do live up to this neon-filled hype, much of the city is composed of surprisingly quiet and charming districts.

Today you’ll experience the quieter side of Tokyo as you embark on a leisurely private cycling tour of the city (urban cycling experience not required). Tokyo is a truly wonderful city for cycling, filled with eclectic neighborhoods along with polite and orderly drivers.

If you’re not interested in cycling, this tour can be modified and made into a backstreets walking tour instead.

Under the guidance of your expert private guide, you’ll wind your way through the slow-paced backstreets of a selection of colorful, off-the-beaten-path neighborhoods. As you explore these non-touristy areas, you’ll also have the chance to stop for casual street snacks along the way.

Your tour will conclude in a lively neighborhood, the perfect place to spend a couple of hours strolling, eating, people watching, or shopping.

After some downtime this afternoon, head out for an incredible sushi meal or a taste of Tokyo’s legendary nightlife.

Sushi chef at authentic sushi shop in Japan

Day 4: Shinkansen (Bullet Train) to Nagano & the Japanese Alps

Enjoy a final morning free in Tokyo with the chance to visit Tokyo’s Tsukiji Market if you wish. While the wholesale section of the fish market moved to Toyosu in 2018, Tsukiji’s lively outer market remains an incredible place to immerse yourself in Japanese cuisine.

Then it’s time to leave the city for the mountains. Today you’ll have your first experience traveling on Japan’s remarkable trains. To begin your journey into the Japanese Alps, you’ll be speeding northwest into central Japan via Japan’s iconic shinkansen (bullet train), a wonderfully pleasant way to travel. Before you depart, take some time to shop for a beautiful bento box lunch to enjoy on the journey (major train stations in Japan offer an astounding variety of delicious seasonal bentos).

On arrival at Nagano Station, you’ll make the easy change to a local train headed deeper into the Alps. But before you continue on your journey, you will have a couple of hours to stroll the charming streets of Nagano City itself.

It’s a pleasant walk (or short taxi ride) from Nagano Station to the magnificent Zenko-ji, one of Japan’s most important temples, with a history of 1,400 years. The small city of Nagano developed around the temple complex, and the streets leading to Zenko-ji are lined with old-fashioned shops.

Leaving Nagano, it’s a short trip by local rail to your destination for the evening. You have the option to stay in a traditional Japanese-style ryokan in a quaint onsen (hot springs) town, or a small and stylish boutique hotel in the beautiful little historical town of Obuse.

Enjoy a relaxing evening in rural Japan in preparation to visit the Snow Monkeys tomorrow morning.

Your Alps ryokan or hotel: Jinpyokaku Honten or Masuichi Kyakuden

Shinkansen bullet train conductor Japan

Day 5: Morning Snow Monkeys & Afternoon Travel to the Kiso Valley

This morning you will have the chance to visit Japan’s iconic Snow Monkeys, before spending the night in picturesque village of Tsumago in the Kiso Valley.

From the entrance to the Snow Monkey Park (Jigokudani Yaen Koen), it’s about a half-hour walk to the onsen where the famous Japanese Macaques bathe. In winter the trail is often covered in deep snow, so you’ll need to dress appropriately!

Following your morning adventure, this afternoon you’ll make the easy trip south by rail into the scenic and historic Kiso Valley.

This afternoon and evening settle into the gentle pace of your rural accommodations, located in the idyllic outskirts of Tsumago village. Enjoy a rejuvenating soak in the healing onsen, a healthy and delicious dinner featuring local and seasonal specialties, and the chance to stargaze before bed.

Your Tsumago ryokan: Takimi no Ie or Fuki no Mori

Baby Snow Monkey (Japanese Macaque) at Jigokudani Yaen Koen in Nagano, Japanese Alps

Day 6: Walk Along the Nakasendo Way from Magome to Tsumago

Enjoy an early morning soak in the onsen and a simple Japanese breakfast before your day hike. Today you’ll have the chance to walk along the Nakasendo Road, one of five routes used by samurai to travel between Tokyo and Kyoto during the Edo period.

You’ll begin in the quaint post town of Magome, which lies on a steep slope and is one of the best-preserved towns in the Kiso Valley. From here, you’ll embark on your hike to Tsumago along one of the most carefully preserved stretches of the Nakasendo (a hike of approximately 3-4 hours).

On arrival back in Tsumago, you’ll have the remainder of the afternoon free. Tsumago is one of the Nakasendo’s most beloved post towns, with good reason. The village’s residents have done their utmost to preserve an Edo-era atmosphere, resulting in one of Japan’s most delightful historical villages.

Magome village, a post town on the Nakasendo Way en route to Tsumago in the Kiso Valley, Japan

Day 7: Morning in Tsumago & Travel to Kyoto

Enjoy your final morning in the Kiso Valley. When it’s time to depart, you’ll travel by rail (including another ride on the shinkansen) to the ancient capital, Kyoto.

Kyoto is one of the most culturally rich cities in the world, and the place most travelers dream of when envisioning Japan. Home to 17 UNESCO World Heritage sites, Kyoto was the capital of Japan for over a thousand years and remains the heart and soul of traditional Japan.

Today it is a large modern city of over a million residents, and at first glance looks almost like any other Japanese town. But the city retains many of its long-established traditions, and despite the neon and concrete prevalent in many parts of town, Kyoto is teeming with beautiful and well-preserved pockets where time seems to move more slowly.

You’ll have part of the afternoon free to settle in and adjust to your new surroundings.

In the early evening, you’ll head out on a fascinating private walking tour through the backstreets of Kyoto’s best-known geisha district, Gion. As you slowly meander your way through the narrow lanes and hidden alleys of this enigmatic district, your expert guide will teach you about the history and reality of Kyoto’s geiko (as geisha are called in Kyoto) and maiko (apprentice geisha).

This is a great way to learn about Japan’s most misunderstood traditional profession, and it’s likely you’ll come across geiko or maiko en route to their evening appointments.

Your Kyoto hotel: Hotel Kanra Kyoto or Hyatt Regency Kyoto

Sunset from Kiyomizu-dera, Kyoto, Japan

Day 8: Private tour to introduce you to Kyoto

While it’s possible to enjoy Kyoto unguided, a local expert guide will undoubtedly enhance your experience in ways you would never imagine. Having a guide to peel away the layers and help you explore the hidden nooks of the city will make your short time in Kyoto much more powerful and meaningful.

The discerning eye will soon pick out Kyoto’s treasures: sacred shrines tucked in among shopping arcades, time-honored teahouses nestled among modern businesses, and charming geiko scuttling down backstreets heading to evening appointments.

Kyoto’s charm lies in these details, and whether you’re here for three days or three years, the closer you look, the more you’ll discover.

Traditional lanterns in the Gion geisha district of Kyoto, Japan

Day 9: Day trip to the Miho Museum

Today you will visit the stunning Miho Museum.

An easy day trip from Kyoto – located in rural Shigaraki – the Miho Museum was designed by the renowned architect I.M. Pei.

An experience all its own, you’ll find awe-inspiring architecture and world-class artifacts from ancient civilizations. While there be sure to eat lunch at the cafe, the delicious meals are prepared using produce grown on the museum’s grounds.

Tunnel at I.M. Pei's Miho Museum, Shigaraki, Japan

Day 10: Travel to the art island, Naoshima

Today you’ll make the journey by bullet train – followed by local train and ferry – to the famous art island of Naoshima.

Naoshima – a small island in the Seto Inland Sea – could easily be another pretty, but forgotten island scraping a living from fishing. However, a unique art project pioneered by the Benesse Corporation, has transformed Naoshima into a world-class art destination.

Today, Naoshima is home to a large collection of contemporary art museums, galleries, exhibits and installations, which offer a tour de force of architectural expression integrating art and the natural environment.

Two of the main museums – the Chichu Art Museum and Benesse House – were designed by the world-famous architect Tadao Ando, and feature works by Claude Monet, Walter de Maria, James Turrell, Andy Warhol, Richard Long and Bruce Nauman, among others.

Honmura, a small port town on Naoshima’s eastern coast, is home to the Art House Project, a collection of abandoned houses, workshops, as well as a temple and a shrine that have been converted into art installations and venues for contemporary art by artists and architects from Japan and abroad.

The art houses are scattered throughout town, and most of them are unassuming from the street, blending into the surrounding traditional Japanese neighborhood. The interior of each, however, has been given over to artists to convert into whatever suits their artistic vision.

Your Naoshima hotel: Benesse House

Pumpkin sculpture by Yayoi Kusama at Benesse House Naoshima Island Japan
Yayoi Kusama’s famous and whimsical Pumpkin sculpture on Naoshima Island

Day 11: Return to Tokyo for final evening

You’ll have part of the morning to enjoy Naoshima, before it’s time to make the return journey to Tokyo.

Enjoy your final evening in Japan!

Your Tokyo hotel: Palace Hotel Tokyo or Conrad Tokyo

Day 12: Depart Japan

You’ll be free until departure. Depending on your flight time, you may have time for some last-minute explorations (and eating!).

In good time for your departure flight, you’ll be picked up at your accommodations for the comfortable private transfer to your departure airport.

You can depart from either of Tokyo’s two major airports, Narita (NRT) or Haneda (HND). This sample trip can also be customized to end with departure from elsewhere in Japan.

Come back to Japan soon!