Japan Rail Pass user guide. How to use JR Pass to its maximum.

It's a new look Japan Rail Pass. (C) JR Rail
It’s a new look Japan Rail Pass. (C) JR Rail

JR Group has made an announcement to change the rule of Japan Rail Pass. Any Japanese citizen will not be able to purchase Japan Rail Pass after April 1, 2017. March 31, 2017 is the last day to purchase Japan Rail Pass for Japanese citizen. The exchange order can be exchanged until June 30, 2017.

Japan Rail Pass (a.k.a. JR Pass) covers all JR lines throughout Japan. This is only rail pass that covers throughout Japan. If you travel even round trip to Osaka from Tokyo, price of 7 days pass almost equal to normal fare. I think this pass gives the greatest deal to the travellers who wants to travel in Japan.

Japan Rail Pass Official site is very informative. But some points are not clear. And also some of you are overwhelmed to read so many pages.

In this post, I tell you about this pass as simple as possible. I compare normal fare and pass, how to choose the retailer, additional charge and many more.

*The information in this article is current at the time of writing.

How to buy

Basically only the authorized agents are allowed to sell Japan Rail Pass. You can find the agent list at this page of Japan Rail Pass official site. These following companies are major distributors.

  • JAL (Japan Airlines / National flagship)
  • ANA (All Nippon Airways / one of two major airlines)
  • JTB (Biggest travel agency in Japan)
  • NTA (Nippon Travel Agency / third biggest and the oldest travel agency in Japan)
  • KNT (Kintetsu International / same group as Kintetsu Railways. Second biggest travel agency)
  • Top Tour (Same group as Tokyu Railway)
  • JALPAK (Same group as Japan Airlines)

JAL and ANA sell the pass to the passenger who take their flight. You cannot purchase only pass from them.

In these days, many companies have a contract with these above distributors And they are selling the pass online as a retailer. If you find the name on the list at the above link, it is an official retailer. If you cannot find it, you should check that company before you buy.

Basically you cannot purchase Japan Rail Pass in Japan. But as I mentioned above, some of the agents sell JR Pass online and they can mail to you by Courier or Express post service even in Japan. So if you have already arrived in Japan as temporary visitor, you may ask the agent in your country and make sure that they can mail it or not.

Types and prices

There are two types, Green and Ordinary, and three duration, 7, 14 and 21 days.

Type 7 days 14 days 21 days
Ordinary 29110 yen 46390 yen 59350 yen
Green 38800 yen 62950 yen 81870 yen

*Child (6yrs to 11yrs) rate is 50% off.

When you purchase it, rates are adjusted by your country’s currency.

Tokaido Shinkansen
If you take Tokaido Shinkansen and Narita Express to Kyoto, Japan Rail Pass should be your choice.

This pass is eligible for the railway, bus and ferry services that are provided by Japan Railways Group with few exceptions. I explained these exceptions later.

In my opinion, Japan Rail Pass offers you the most unbeatable deal. There are many kinds of rail passes in Japan, such as JR East Pass, JR Hokkaido Pass, JR Kyushu Pass and many more. But Japan Rail Pass is only rail pass that covers throughout Japan. And of course it covers both Tokyo and Kyoto. But if you need the detail information about other passes, please access to the category, Other Rail Passes. I wrote about many other rail passes in the posts.

7 days pass price is almost same as round trip of Tokyo – Osaka

If you will have round trip between Tokyo and Osaka, Japan Rail Pass 7 days is recommended.
One way base fare and Shinkansen surcharge from Tokyo to Shin-Osaka – 14140 yen

So if you have round trip between Tokyo and Osaka, single fare is slightly cheaper, but you will get some chances to take a train in Tokyo, Osaka or Kyoto. And Japan Rail Pass is more flexible and much easier to handle.

If you need some more information about price comparison, please see “Compare to regular fare”. You will see some example.

If you will have only one way trip between Tokyo and Osaka, single fare is your choice. I wrote about using single ticket at the post, For non JR pass travellers. Guide to use JR single ticket, basic rules, validity and stopover.

Green seat on Super Ozora by 283 series (C) Sonic Rail Garden
Green seat on Super Ozora by 283 series in Hokkaido (C) Sonic Rail Garden

What is the difference between Green and Ordinary.

Green Class is like business class seat. It was the first class in all Japan Railway’s trains. But since Tohoku Shinkansen Hayabusa started to run, Gran Class that is upper class than Green Class was introduced. As a result, Green class became the second highest seat in all JR trains.

If you take Gran Class by Japan Rail Pass, both Ordinary pass and Green pass cover only basic fare. You need to pay Limited Express surcharge and Gran Class fee. Please see the post, Japan Rail Pass can be used for Hayabusa to get details.

Advantage of Green Class seat is space and atmosphere. Green class seat it more spacious and quieter than ordinary seat. Shinkansen and most of Limited Express have this class. Even some local trains, such as Rapid trains in greater Tokyo area have Green Class seat too. Please read one of my post, Worthwhile buying Japan Rail Pass Green Pass?. I explained the details about Green class seat in this post. I hope it may help you to decide which pass you purchase.

By the way Green surcharge is calculated based on distance. But the rate differs with types of train and companies. For example, Green class surcharge is 2000 yen for Narita Express from Narita airport to Greater Tokyo area, 5150 yen for Shinkansen from Tokyo to Kyoto or Osaka. So if you have a round trip from Narita airport to Kyoto, Green pass still give you greater value.

If you really care about the budget, Ordinary class is fine. I am sure you will be satisfied with that. It is way better than economy seat on the flight. My height is 6’1″ (184 cm). But I have never had a problem with the leg space.

How to exchange

Exchange order
Exchange order

You can get “Exchange Order” at the time of purchasing. It is not an actual pass but a voucher. You have to exchange for an actual pass after you arrive in Japan. The validity of exchange order is three month from the date of issue. The pass will never be sold out. So don’t buy it too early.

Exchange place
You will find the sign in English very easily.

Exchange Order can be exchanged at the designated station. Narita airport, Kansai airport, Tokyo, Shinagawa, Osaka, Kyoto and more than 40 major stations throughout Japan are on the list. You can find the station list at Japan Rail Pass official site.

When you turn in, go to the station where I mentioned above, and show your passport and exchange order. You will get the application form and fill in.

When you turn in the pass, you can choose the first day of use within one month from this day. And you will receive the actual pass with stamped that shows the start and finish dates. So technically the earliest day to purchase the exchange order is four month prior to your first day of use.

By the way, the definition of “1 day” is 00:00 to 23:59. If you start to use 7 days pass on April 1, your pass is expired at 23:59 on April 7. However if you are on board at 0:00 on the last day, you still can take a train. Your pass cover until you get off the train. After you get off the train, as long as you don’t exit the station, your pass still cover basic fare.

ex)
If you use 7 days pass, sample itinerary below can be covered by the pass.
Day 7 Take Sunrise Seto at 23:55 at Himeji
Day 8 Arrive Tokyo at 7:08 and continue to travel to Narita airport by Airport Rapid train

Validity

Japan Rail Pass is valid for the railway service, bus service and the ferry service. Japan Rail Pass cover all trains that are operated on those lines with some exception. But most of trains are covered by Japan Rail Pass. You can go almost anywhere throughout Japan except Okinawa. (Any JR companies do not offer any services in Okinawa.)

Let’s see that we CANNOT get on by Japan Rail Pass.

Tokaido Shinkansen

Nozomi (=のぞみ) / Mizuho (=みずほ) on Tokaido, Sanyo and Kyushu Shinkansen

Nozomi is the fastest and most frequent operated train on Tokaido-Sanyo Shinkansen between Tokyo, Kyoto, Osaka, Hiroshima and Fukuoka. Mizuho is the fastest train between Shin-Osaka and Kagoshima-Chuo. Japan Rail Pass is NOT valid for these trains. Even a basic fare to take Nozomi or Mizuho is not covered by Japan Rail Pass at all. If you want to take Nozomi or Mizuho, you have to pay full fare.

I understand this is the disadvantage. But you can take Hikari or Sakura that is the second fastest train. I haven’t had any problem with that.

ex)
Time of travelling between Tokyo and Shin Osaka — 3 hours by Hikari / 2.5 hours by Nozomi
Frequency — 2 trips of Hikari every hour / 5 trips of Nozomi every hour
*There are some more trips of both Hikari and Nozomi in peak hours.

Please refer one of my post, Tokaido-Sanyo Shinkansen to get the details abut the difference between Nozomi and Hikari.

Mizuho is the fastest train on Sanyo Shinkansen and Kyushu Shinkansen. This train was introduced on Mar 12, 2011 when Kyushu Shinkansen had been completed. JR West and Kyushu started to operate new train service Mizuho and Sakura bewtween Shin-Osaka and Kagoshima-Chuo. Sakura is the second fastest train on Sanyo and Kyushu Shinkansen. You can take this train service by Japan Rail Pass.

Gran Class of Tohoku, Hokuriku and Hokkaido Shinkansen

Gran Class seat on E5 series (C) Sonic Rail Garden
Gran Class seat on E5 series (C) Sonic Rail Garden

Japan Rail Pass covers Tohoku, Hokkaido and Hokuriku Shinkansen trains fully. Gran class that is the highest class seat is available on these Shinkansen lines. This class is first ever seat higher than Green class. If you take this Gran class, both Japan Rail Pass Ordinary and even Green cover a base fare only. You need to pay all amount of surcharge beside JR Pass.

Delux Green on JR Kyushu trains

Some of limited express trains in Kyushu have Delux Green Class. If you take this class, you have to pay both Limited Express surcharge and Delux Green surcharge. Even Green Pass do not cover both surcharge.

Green Private Compartment

Green compartment on Super View Odoriko (C) Sonic Rail Garden

These following trains have Green compartment.

If you use this type of seat by Japan Rail Pass, your party must be 4 persons because it is based on 4 person. If you use this by 3 persons or less, you have to pay surcharge for insufficiency.

Overnight train / Sleeper car

Any type of Japan Rail Pass cover only a basic fare for the sleeper car. So you have to pay the accommodation fee (berth and compartment) and limited express or express surcharge. But there are two overnight trains, Sunrise Izumo and Sunrise Seto that you can get on by Japan Rail Pass with no extra charge. Because these overnight trains have the specialized accommodation that is called “Nobi Nobi seat”. Please see the posts, Sunrise Izumo and Sunrise Seto to get the detailed information.

Trains run through Non JR lines

Some of limited express trains go through Non JR lines. You need to pay some extra for the section where your train goes on Non JR line. Because Japan Rail Pass cover only JR lines. The following list shows you the train go through Non JR lines. Please refer each trains’ page to get the details about the extra charge.

Bus services

There are 8 bus companies in JR Bus Group. But these bus companies are different from train service companies now. These eight companies operate local bus service and highway bus service. But Japan Rail Pass covers a few local bus services only.

JR’s local bus services are a sort of commute service. I pick up some lines for the tourist.

Japan Rail Pass may cover some more bus services. But even official site does not provide any detailed information. As far as I know, I can confirm that JR Pass covers only these bus services.

Ferry Service

Miyajima ferry service is operated between Miyajimaguchi and Miyajima. Japan Rail Pass is valid for this route. Miyajima is UNESCO world heritage site and one of the most popular destination for foreign travellers. This ferry cruise is very short trip. It takes only 10 minutes. Please refer one of my post, How to get Miyajima to get the details about Miyajima.

JR Kyushu operates the international ferry service between Hakata and Busan (Korea) But this is NOT valid for Japan Rail Pass.

Other train services

Japan Rail Pass does not cover any NON JR train services, such as the subways (Tokyo, Kyoto, Osaka, Nagoya, Sapporo, Yokohama, Sendai, Fukuoka), other train services by private companies, city bus services, local bus services and ferry services. The following list shows you major train services that Japan Rail Pass does not cover.

  • Sapporo Subway
  • Sendai Subway
  • Tokyo Subway
  • Yokohama Subway
  • Keihin Kyuko Railway (a.k.a. Keikyu, Shinagawa-Haneda-Yokohama)
  • Keisei Railway (Narita airport-Chiba-Ueno)
  • Tobu Railway (Asakusa-Nikko/Knugawa Onsen)
  • Odakyu Railway (Shinjuku-Hakone/Enoshima)
  • Izu Kyuko Railway (Ito-Shimoda)
  • Fuji Kyuko Railway (Otsuki-Kawaguchiko)
  • Nagoya Railway (a.k.a. Meitetsu, Chubu airport-Nagoya-Gifu)
  • Nagoya Subway
  • Kyoto Subway
  • Osaka Subway
  • Nankai Railway (Namba-Kansai airport/Koyasan/Wakayama)
  • Kintetsu Railway (Namba-Nara/Kyoto/Ise/Nagoya)
  • Hankyu Railway (Kobe-Umeda-Kawaramachi,Kyoto)
  • Keihan Railway (Yodoyabashi-Sanjo,Kyoto)
  • Hanshin Railway, Sanyo Railway (Umeda/Namba-Kobe-Himeji)
  • Fukuoka Subway
  • Nishitetsu Railway (Tenjin-Dazaifu)

Tokyo Monorail between Hamamatsucho (Tokyo) and Haneda airport is not JR train but this is owned by JR East and it is covered by Japan Rail Pass.

The following trains and segments are non JR lines. But those are covered by JR Pass.

  • Local and rapid trains on Aoimori Railway between Hachinohe and Aomori. But you cannot make a stopover except Hachinohe, Noheji and Aomori
  • Local and rapid trains on Ainokaze Toyama Railway between Toyama and Takaoka. But you cannot make a stopover except Toyama and Takaoka (after March 14, 2015)
  • Any trains on IR Ishikawa Railway between Kanazawa and Tsubata. But you cannot make a stopover except Kanazawa and Tsubata. There are direct trains from Kanazawa or Osaka to Wakura Onsen. These trains are go through this segment and then go on JR Nanao line. If you take these trains, extra charge is not required on top of JR Pass.

Who is eligible?

If you are an foreign tourist, you have to be “Temporary Visitor”. This entry status will be stamped at immigration on your passport. Other status cannot be acceptable. Be careful. You have to show your passport at the station when you pass your exchange order to get actual pass.
If you are already in Japan as other status, you have to change your status first. Otherwise you cannot buy Japan Rail Pass. Please see “How to buy and exchange”.

If you are Japanese citizen who have permanently status in foreign country, or who married to a non-Japanese, you are qualified.
JR Group has made an announcement to change the rule of Japan Rail Pass. Any Japanese citizen will not be able to purchase Japan Rail Pass after April 1, 2017. March 31, 2017 is the last day to purchase for Japanese citizen. The exchange order can be exchanged until June 30, 2017.

How to refund

You can refund within one year from issue date before you turn in for the actual pass. Simply bring or send your exchange order to the agent where you purchased it. They will subtract a handling fee and refund to you. The handling fee is usually 10% of the amount. Contact to your agent and make sure it before you refund.
You can NEVER refund after turned in the actual pass.

Lost or Stolen

Once you lost it, it’s over. Either an exchage order or an actual pass cannot be reissued. Be carefule to use!

1,015 thoughts on “Japan Rail Pass user guide. How to use JR Pass to its maximum.”

  1. dear takeshi,
    me and my wife are planning to go to japan this may 2017. is it possible to use the 7day pass for: fukuoka>kyoto>osaka>tokyo>back to fukuoka?
    or is it too much?

    thank you,
    carlo

  2. Hello Takeshi,

    I will be staying in Tokyo from February 20-26. What line do I take to get to Mt. Fuji? Thank you for any help!

    Brandon

  3. Hi Takeshi,

    I plan to travel with my wife from the 14th to the 20th of this month to Tokyo and Kyoto. Please suggest if JR ordinary pass will be useful and whether can be used on Tokyo-Kyoto Sinkansen?
    Regards
    Sushant

    1. Hi Sushant,

      Yes. But you must have round trip between Tokyo and Kyoto. Because one way fare and Shinkansen surcharge is almost half cost of 7 days JR pass. If you have one way trip, single fare is your choice.

      Cheers,

      Takeshi / JPRail.com

      1. Hi Takeshi san,

        It is indeed a round trip. One more thing, I have the JR pass and I understand that Nozomi shinkansen is not valid on this pass. So how do I recognise the hikari shinkansen? as I understand from some pieces of information, the shinkansen are differently coloured? so what colour is the Hikari one?

        cheers
        Sushant

  4. Hi Takeshi,

    We are a party of 2 and are looking at purchasing a Green pass for 7 days but are not sure if this will get us in trains with a green car.

    Tokyo to Hakodate
    Hakodate to Yokohama
    Yokohama to Hiroshima
    Hiroshima to Huis Ten Bosch
    Huis Ten Bosch to Osaka

    Will we be able to get on a train with a green car for all these trips and is it good value?

  5. Hi Takeshi-san,

    Thanks for this clarification. One final question: would the JR Green Pass cover part of the Gran Class surcharge on the Shinkansen, i.e., would the JR Green Pass contain the Green Class surcharge already, so that one pays the difference between the Gran Class and Green Class surcharges?

    Kind regards,
    Arend

    1. Hi Arend san,

      JR Pass Green does not cover Gran class charge. And it covers only base fare if you take Gran class. You need to pay full charge of Gran class seat fee and express surcharge, not difference between Gran class and Green class. It covers only base fare unfortunately in this case too.

      Cheers,

      Takeshi / JPRail.com

  6. Thanks very much, Takeshi-san
    This was very helpful. We may travel to Otaru, but we have no plans to travel to eastern or central Hokkaido, so I think we will go for the JR East-South Hokkaido pass, as you suggest.
    We will land at Haneda at mid-afternoon, andwe can make our purchase/exchange there.
    Meanwhile, I have narrowed down our train selection to the following:
    08 Feb: Shinkansen Habusa 13 from Tokyo to Shin-Hakodate-Hokuto – Gran Class
    09 Feb: Ltd Exp Super Hokuto 11 from Hakodate to Noboribetsu – Green Class
    10 Feb: Ltd Exp Super Hokuto 11 from Noboribetsu to Sapporo – Green Class
    Based on these selections, I arrive at a total savings – using the above pass – of about 8,000 yen per person, compared to buying individual tickets all the way. Could that be correct?
    Thanks for your efforts!
    Kind regards,
    Arend

    1. Hi Arend san,

      I think this pass is not a right choice.
      Because if you take Gran class and Green class seats, the pass covers only base fare part. It costs actually 15,000 yen. You have to pay full fare for express surcharge + seat fee. This additional cost is not the difference between ordinary seat and Green/Gran class.

      So single ticket is much better choice actually.

      Cheers,

      Takeshi / JPRail.com

  7. Hi Takeshi-san,

    Thanks for all the rail travel information you have put online, your detailed articles have already been a great help. Still, I would like to ask a few questions.

    We are a group of four (from France, Bulgaria, and Holland, two of us taller than 1.85 m) planning a Japan trip with the following itinerary:
    Feb 05 Arrival at Tokyo Haneda for short stay, hotel near Tokyo Station
    Feb 08 Tohoku Shinkansen to Shin-Hakodate-Hokuto; train to Hakodate
    Feb 09 Train to Noboribetsu
    Feb 10 Train to Sapporo
    Feb 13 Departure from New Chitose Airport

    From Feb 01, it should be possible for foreigners to order tickets online for the 10:44 Hayabusa from Tokyo all the way to Shin-Hakodate-Hokuto (currently only to Shin-Aomori). For this special occasion, we would like to

    travel Gran Class (and pay for the Gran Class upgrade). Will the Gran Class option also be available online?

    For our case, what would be the best Rail Pass option, in your opinion? Japan Rail Pass (plus Limited Express/Gran Class surcharge), Japan Rail Pass Green (plus Gran Class surcharge), or the JR East-South Hokkaido Rail Pass (plus Green Car & Gran Class surcharge)?

    I hope to be able to buy our Exchange Orders (for the Rail Passes) and all the train tickets in advance. It seems that Hyperdia only allows planning of the various rides, but for the ticket purchase I need to visit other sites. Is this correct? And will I be able to collect the Rail Passes and tickets at the Haneda Airport International Terminal?

    Will the Rail Pass cover the transfer from Haneda Airport to Tokyo Station?

    And finally: which pass would be best to cover three days of sightseeing in Tokyo. It seems to me that the Tokyo Subway 72-hour ticket would do fine. What do you think?

    Thanks in advance for your efforts!

    Kind regards,

    Arend

    1. Hi Arend san,

      I recommend you to use JR-East South Hokkaido Rail Pass if you are sure to ride Gran class on Shinkansen. If you want to take Green on Shinkansen and other trains, JR Pass Green is the best choice.

      And also you have to think about the plan when you are in Sapporo. If you stay in city of Sapporo or trip to Otaru, JR-East South Hokkaido pass is okay. But if you travel eastern and central Hokkaido, like Furano, Asahikawa, JR pass is your choice. Only JR pass covers these area.

      You can purchase/exchange your pass in Haneda. But service hour is very limited.
      http://www.jreast.co.jp/e/customer_support/service_center_haneda.html

      If you can’t use this, you have to pay single fare to get Tokyo station.
      http://www.jreast.co.jp/e/customer_support/service_center_tokyo.html

      Subway ticket covers most in Tokyo but you still can use JR pass or JR East South Hokkaido rail pass to visit many places in Tokyo.
      http://jprail.com/destinations/kanto-area/tokyo-kanto-area/guide-to-take-trains-in-tokyo-how-to-choose-the-best-deal-and-the-best-route-by-train-to-get-the-major-spots.html

      Cheers,

      Takeshi / JPRail.com

      In JR East reservation site, you can book Gran class too.

  8. Hi, Takeshi-san.

    Pardon my ignorance. This is off topic but I am planning to use regional pass instead of nationwide JR Pass.

    I was thinking of 2 scenarios:
    1. Use JR Pass then either 3 or 5-day All Kyushu Pass; and
    2. Combination of All Kyushu Pass by JR Kyushu and Sanyo San’in Pass by JR West.

    I was reading various forums and websites and many have done purchasing more than 1 pass, especially for nationwide JR Pass, without overlapping periods which should be. Some are even combining JR Pass with regional pass.

    There is no doubt that combining a regional pass will make sense after JR Pass’ expiration. The question is, are regional passes of different group like the scenario 2 above will allow me to overlap a period say even for 1 day only? The thing is that I plan have a base in Tottori coming from Kumamoto. The regional passes will be purchased outside of Japan.

    I would appreciate your feedback. Thanks!

    1. Hi Jini san,

      It’s completely no problem to use two different passes. But even if you purchase it online, you still need to exchange the actual pass. So when you travel from Kumamoto to Tottori, you must have two actual passes in your hand. Otherwise you have to get off the train at Hakata and exchange it.

      You can exchange Sanyo Sanin area pass at Hakata or Kokura station in Kyushu. When you can drop by these station before trip to Tottori, you can exchange it in advance.

      Cheers,

      Takeshi / JPRail.com

  9. Hi Takeshiさん.
    I want to ask, we can exchange and reserved at Kansai Airport right?
    But the reserve seat only once, can’t multiple place, is it right?
    Like at Haneda.

    I mean when arrive at KIX, I want directly using the JR Pass and reserve many train (after exchange). I wonder where is the near place I can reserve the seat at Midori no Madoguchi.

    Thank you before.
    Nan.

    1. Hi Nan san,

      I’m not sure that I understand your inquiry correctly. Anyway you can exchange and book at Kansai airport station.
      You can book your seat when you exchange the pass or later. Midori no Madoguchi is located at most of major JR stations. You can book it at any Midori no Madoguchi. You can complete all bookings at Kansai airport station. Of you can book for some trains only at Kansai and make another bookings later at other stations.

      Cheers,

      Takeshi / JPRail.com

      1. Takeshiさん thank you for your reply and my bad (=_=)

        I mean, last year when I arrived at Haneda airport and exchange the JR Pass, I only allowed to made my first reservation at the counter.
        I can’t book another reservation, so I wonder is it same method at Kansai Airport, because I really want book many reservation on first day I arrive at KIX.

        Sorry for confusing.
        Nan.

        1. Hi Nan san,

          I have never heard that. Probably Haneda airport travel desk was busy and they made some restriction.
          I usually exchange the pass at Narita. I always complete all bookings at once. I have made more than 20 bookings before. Kansai airport station has been very busy in these days. They may make same restriction as Haneda. But I have never heard that at this point.

          Cheers,

          Takeshi / JPRail.com

  10. Hi Takeshi,

    I would need some information for JR pass, i’ve already bought a 7 days pass. Can I use it for below destination:

    Narita – Tokyo – Narita
    Tokyo – Osaka – Kyoto – Tokyo
    Tokyo – takaragawa onsen – Tokyo

    Which train (name) that we can use?

    1. Hi Natasha,

      All trips are covered.

      Narita – Tokyo – Narita
      You can take Narita Express.
      http://jprail.com/trains/sort-by-type/limited-express/narita-express.html

      Tokyo – Osaka – Kyoto – Tokyo
      Hikari on Tokaido Shinkansen is your choice.
      http://jprail.com/trains/sort-by-departure-arrival-stations/stations-in-tokai/nagoya-toyohashi/what-is-shinkansen-bullet-train.html

      Tokyo – takaragawa onsen – Tokyo
      I think Jomokogen station is the gateway. But you need to take shuttle or taxi from this station or Minakami station. If you go to Jomokogen, you can take Joetsu Shinkansen:
      http://jprail.com/trains/sort-by-departure-arrival-stations/stations-in-kanto/tokyo/ueno/joetsu-shinkansen.html

      Please ask your hotel in Takaragawa onsen which station your hotel can pick you up. If you need to go to Minakami, you still can take Joetsu Shinkansen but you have to get off at Takasaki and need to change to local train to Minakami.

      Cheers,

      Takeshi / JPRail.com

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