Japan by Rail: Sample of a Custom Itinerary

Advisor - Lee Libro
Curated By

Lee Libro

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  • Japan

  • Active Travel

  • Arts & Culture

  • Couples Travel

  • Food & Wine

  • Sightseeing

  • Local Culture

  • History

A woman in traditional Japanese dress holding a red umbrella.
Curator’s statement

Traveling through Japan independently with a custom itinerary offers an immersive way to experience the dignity and deeply traditional culture of Japan. For those wanting flexibility and a well laid out balance of activity, a custom itinerary can provide both structure and freedom. Experience the many diverse aspects of Japan along the way. This example takes you from the organized city life of Tokyo to the wild streets of Dotonbori in Osaka to the ancient shrines and mountains of Kyoto and a relaxing mountain retreat in Hakone…an ideal itinerary for one’s first time in Japan.

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Where to stay

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Conrad Tokyo

Exceptional service and a killer location in the Minato District are just two highlights of this best-in-class city sleep.

Fora Perks
  • $100 hotel / resort credit.

  • Breakfast daily.

  • Upgrade & extended check-in/out whenever possible.

Keio Plaza Hotel

Upscale property in central Tokyo with high-end rooms and suites offering city views.

Hyatt Regency Hakone Resort And Spa

Experience Japanese tranquility and modern luxury in Hakone, where soothing hot springs, scenic beauty, and Hyatt's hospitality create a rejuvenating stay.

Fora Perks
  • $100 hotel / resort credit.

  • Breakfast daily.

  • Upgrade & extended check-in/out whenever possible.

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Advisor - Lee Libro

Unlock perks by contacting Lee to book your trip.

Day 1: Arrive in Tokyo

Lit city buildings at night.

Upon Arrival at Narita Airport, after gathering luggage and going through customs, go to the JR East Travel Service Center in Terminal 2, Level B1F to exchange your JR Pass Voucher (I will have provided this for you), and then prebook Odawara-Kyoto and Osaka-Tokyo Bullet Train Tickets. The rest of all rail travel will be on the fly as you please, using your JR pass or Suica cash card (Vouchers will have been pre-ordered.)

After transferring into Tokyo and arriving at your hotel, either rest or set out to explore. For the purposes of this itinerary, we have you located in Shinjuku. Spend the evening exploring Shinjuku or relax at the Keio Plaza hotel where every night you can enjoy complimentary cocktails, appetizers and the view from the Club Lounge as part of your Premier Grand King reservation; the choice is yours.

Day 2: Tokyo

Brown Japanese style shrine building during daytime.


Daily Breakfast for two included in reservation – at The Club Lounge on the 45th floor with views over the city - an amazing buffet with both western and eastern choices.

9am - 11 am

Just a block away from the hotel, catch the Red Bus Tour for a quick overview of the western prefectures of Tokyo - from Shinjuku to Tokyo Station.

Stops will be at Harajuku, Tokyo Tower, Shiba Park, Meiji Shrine, Nippongi, Shibuya and Tokyo Station.

Use your JR Pass From Tokyo Station to catch the JR Chuo line back to Shinjuku.


A sushi conveyor belt restaurant, Sushiro, in Shinjuku is a win!


Free Time! Possibly return to the hotel for the complimentary afternoon tea at the Club Lounge, then refresh before dinner.


After complimentary cocktail hour at the Club Lounge explore Shinjuku at night followed by dinner at one of the many choices in Shinjuku (See my Tokyo Restaurant recommendations).

Day 3: Exploring Tokyo

A tray with raw fish pieces.


After breakfast CHOICE: Use your JR Pass from Shinjuku Station to Tokyo Station - Explore Ginza shopping followed by train to Tsukijii Fish Market for lunch.


Train from Shinjuku to Harajuku and then back on train two stops over to explore Shiba Park for a peaceful respite from the city (It’s possible to do both depending on your pace.)


I recommend timing so that your lunch time is at Tsukijii Fish Market (See my recommendations for the best sushi and sashimi in the market.)


Open - The Hotel’s complimentary daily tea and cocktail hours are always an option.


Try any number of restaurants in Tokyo, for ramen, okonomayaki, beef, or sushi. (See my dining recommendations) After dinner, stroll from Shinjuku station for drinks at Golden Gai Alley. The return walk to the hotel from Golden Gai alley is just under a mile.

Day 4: Nakamise Dori

City street with people.


CHOICE: Use your JR Pass to take the Train from Shinjuku Station to Asakusa with transfer at Tokyo Station. See Sensoji Shrine, Shop Nakamise-Dori for great souvenirs. Nakamise Dori is a shopping street that dates back to the 17th century with some of the same families running business there for centuries. Don’t miss having Green Tea Ice Cream or a variety of green tea products.


Stop along the way to Tour Imperial Palace - Explore the Palace with a pre-booked tour or simply stroll through the exterior grounds which are open to the public.


Take the train to Shibuya for lunch. See my Restaurant Recommendations.


Do the Shibuya Scramble - Walk with the crowds across the Shibuya Crossing (I know it’s tourist basic... but a must do) followed by a visit to the Hachiko statue in front of the Shibuya Station north exit.

Visit the Shibuya Sky observatory at the Shibuya Scramble Square Building for sunset. Tickets are available the same day on Floor 14. Best to purchase same day rather than prebook online in case you hit a rainy day and change your mind. Only on a clear day can you see all the way to Mt Fuji.


Explore the izakaya dining and drinking options at Nonbei Yokocho (dining alley), next to the Shibuya Station. It’s very similar to Golden Gai Alley in Shinjuku. If you are looking for larger or finer eating establishments, see my Restaurant Recommendations.

Day 5: Romance Train to Hakone

Lake with mountains.


After breakfast, check out of your Tokyo hotel and walk through the subway tunnel to Shibuya Station. Navigate to the Odakyu Line platforms for your Pre-booked Romance Express Bullet Train to Hakone.

Upon arrival at Hakone-Yumoto Station, catch the local bus to Kowakudani Station where your hotel shuttle will be waiting.

HOTEL Choices

A small boutique hotel with luxurious modern rooms, each with private open air hot spring baths in a forest setting, all centered around an early 20th century residential complex.

  • Hakone Suishoen Hotel


  • Hyatt Regency Hakone Resort & Spa


The hotel shuttle will drive you to a restaurant for lunch. I recommend Nakamura for amazing, homestyle Soba. It’s also located across from the Hakone open air Art Museum, where you’ll find modern sculptures, a Picasso museum, outdoor interactive displays, playgrounds, gift shops, and even a hot spring footbath.

After 3:00 pm Call Suishoen Hotel for return shuttle ride. Check-in to your beautiful room with private hot spring bath. Enjoy your relaxing rotenburo (open-air hot spring bath) at your leisure.


A traditional Japanese Kaiseki style meal served at the onsite restaurant Momiji. Optional Yucata robes and traditional footwear are provided in your room for wearing to all dining at Momiji.

Day 6 and Beyond

A collage of four photos from Japan.

After experiencing your restful rotenburo (private open air hot spring bath) at your traditional onsen in Hakone, enjoy traditional Kaiseki cuisine and see the sights of Mount Hakone and Lake Ashi, additional days on your custom itinerary can take you on a shinkansen (bullet train) to Kyoto, Osaka and beyond.

Fortuitously, due to an agreement with the West during WWII, Kyoto was spared bombing. As a result Kyoto is home to 17 UNESCO World Heritage sites. See some of the most beautifully preserved mashiya architecture in the Gion district, visit the Kiyomizudera Temple, the Kinkakuji Temple or the much-photographed Arashiyama Bamboo Forest. Don't miss hiking to the summit of Fushimi Inari where you can leave the crowds in the Tori Gates behind and take in the quiet of misty forest groves and the many Kitsune shrines that lay therein. The Kyoto leg of your itinerary is rich with options, which we can further discuss.

Visit Osaka, often referred to as the Kitchen of Japan, for fun nightlife and an array of food choices from traditional Japanese, Kobe Beef, Conveyor Belt Sushi, Street Foods such as Okonomiyaki, to choices from other ethnicities as well such as Thai and Indian. Osaka is also home to one of the world's largest aquariums, well worth a half day visit. Using Osaka as a hub, there are also many day trips one can do, including Nara, a temple complex teaming with the sacred deer who will greet you, (and even chase you for a coveted snack). The town of Kobe is also nearby, as is the continuation of your journey to visit Hiroshima and Nagasaki if you so choose.

Whether you are looking to book a week or a month in Japan, I can design a custom itinerary that will immerse you in the heritage and beauty of Japan. Using the JR Pass to explore Japan gives you the flexibility to start and end each day as your energy level will dictate, because traveling Japan independently can be taxing. It requires self-reliance, confidence, and in some cases mental and physical stamina. If you have the right tools, such as a custom itinerary, A JR Pass, portable WIfi and some recommended navigational apps, but most of all a travel advisor who will act as your concierge should you need anything along your journey, Japan offers a glimpse into a world full of wonder unlike any other.

For a complete custom itinerary, contact Lee Libro at Fora.

Need to Know

For more travel tips, check out Fora Advisor Judy & Glenn Tudor’s guide, Best New Four Seasons Tokyo Hotel.

Advisor - Lee Libro

Travel Advisor

Lee Libro

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This guide is part of our ongoing series on travel to Japan.