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Regarding this question: in general, what are the rules governing stopovers for JR trains if one does not use a rail pass? A stopover means you have a ticket from stations A to B (say, Tokyo to Hiroshima) and you disembark and exit the ticket gates at an intermediate station (say, Kyoto).

(Spoiler alert: it's complicated.)

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+200

In a nutshell

  1. Only base fare tickets allow stopovers (途中下車, tochū gesha); tickets for additional fees such as limited express fees and seat reservation fees do not.
  2. In addition, only base fare tickets for trips of over 100 kilometers allow stopovers.
  3. However, base fare tickets for travel within one of five special city zones (Tokyo, Osaka, Fukuoka, Niigata, Sendai) do not allow stopovers, regardless of the length of the trip.
  4. The ticket must be used within its validity period; when the validity period of a ticket is over, it ceases to be valid regardless of whether you have reached your final destination. (However it is possible to obtain a refund for the unused section if it is over 100 kilometers, minus a handling fee of 220 yen.)
  5. Backtracking is strictly not allowed, even by just one station. You must always travel in the same direction.

Example

Suppose I am in Tokyo and i want to go to Hiroshima. However, I would also like to spend some time in Kyoto on the way. Because Tokyo to Hiroshima is 894 kilometers, a base fare ticket will allow stopovers, and moreover it will be valid for six days, so I can spend at most five nights in Kyoto.

The first thing I do when leaving Tokyo on day 1 is buy a base fare ticket from Tokyo to Hiroshima, which costs 11,660 yen. Also, because Tokyo to Kyoto is a long trip, I decide to take the Shinkansen, so I buy a separate ticket to pay the additional Shinkansen fees. I can buy an unreserved, reserved, or Green ticket; say I buy an unreserved one, it's 4,870 yen. When entering the Shinkansen gates at Tokyo station, I insert both tickets together, and likewise when exiting at Kyoto. Upon exit at Kyoto, my base fare ticket is returned. I do not use it again until leaving Kyoto for Hiroshima on day 6. (If I do any JR travel while in Kyoto, I buy individual tickets or use an IC card.)

When leaving Kyoto on day 6, I again buy an unreserved Shinkansen ticket to Hiroshima, which costs 4,090 yen. I again use both tickets to enter the ticket gates in Kyoto. Upon exit at Hiroshima, since my trip is now over, both tickets are retained.

I paid a total of 20,620 yen. Had I bought Tokyo-Kyoto and Kyoto-Hiroshima tickets separately, I would have paid 23,650 yen, so I saved over 3,000 yen, the price of a very good meal or a very cheap hotel night.

This example illustrates the basic principle: the base fare for an entire trip (here, Tokyo to Hiroshima) can be paid all at once, within some constraints, whereas any additional fees must be paid on a per-train basis.

When are additional fees necessary?

A base fare ticket alone allows travel on local (普通) and rapid (快速) trains, in ordinary class and on non-reserved seats. In all other cases, additional fees are required:

  • On express (急行) and limited express (特急) trains, including Shinkansens and the overnight Sunrise Seto/Izumo, for all seats. However, no additional fees are required for ordinary non-reserved seats between Miyazaki and Miyazaki Airport, between Aomori and Shin-Aomori, and between Shin-Yubari and Shintoku.
  • On reserved and Green seats in local and rapid trains. Keep in mind that some rapid trains are all-reserved.

How to buy?

Doing this requires to be able to buy base fare tickets and additional fee tickets separately, which is usually done at ticket offices, but can also be done at ticket machines and online. In fact, JR East's English reservation service issues reserved seat tickets only, and it is always necessary to pay for the base fare separately (possibly with a rail pass). JR Hokkaido's English service, however, does not allow this. Some useful words at the ticket office:

  • Base fare ticket: 乗車券 (jōshaken)
  • Shinkansen: 新幹線
  • Limited express ticket: 特急券 (tokkyūken)
  • Non-reserved seat: 自由席 (jiyūseki)
  • Reserved seat: 指定席 (shiteiseki)
  • Green seat: グリーン席 (gurīnseki)
  • GranClass seat: グランクラス席 (gurankurasuseki)
  • Reserved seat ticket: 指定席券 (shiteisekiken)
  • "Only": のみ (nomi)
  • Today: 今日 (kyō)
  • Tomorrow: 明日 (ashita)
  • April 20: 4月20日, or just 4/20 or 4.20 (change accordingly)

In order to describe the desired ticket(s) efficiently, I find it useful to make a quick diagram on the notes application of my phone. For example for the Tokyo-Kyoto-Hiroshima itinerary above, if I only want to buy the Tokyo-Kyoto Shinkansen ticket at Tokyo station together with the base fare ticket, I do the following (station names can also be written in English).

今日

東京
|  新幹線、自由席
京都
|  乗車券のみ
広島

To buy the Kyoto-Hiroshima Shinkansen ticket at Kyoto, proceed normally but mention that you want to buy the limited express ticket only (特急券のみ). For unreserved seats, only the day of usage is necessary, and not the departure time of a particular train: unreserved seat tickets are valid for one day, and can be used on any train on that day.

Validity period of base fare tickets

The validity period of a base fare ticket is a function of the distance traveled, as shown for example by Hyperdia in the headers section of a displayed route in the search results page. Non-integer distances are always rounded up. The validity period of tickets is based, as usual, on calendar days, and not on 24-hour periods.

  • Tickets for travel of up to 100 kilometers and for travel within one of the five special city zones mentioned above are valid for one day (and do not allow stopovers).
  • Tickets for travel of 101 to 200 kilometers are valid for two days.
  • Tickets for travel of 201 to 400 kilometers are valid for three days.
  • Tickets for travel of 401 to 600 kilometers are valid for four days.
  • And similarly an extra day of validity is added per chunk of 200 kilometers.

The simple formula for trips of over 100 kilometers: divide the distance by 200, round up, and add one day.

There is no limit on the number of stopovers which can be made within the validity period of the ticket (and within all the other constraints). For example, with the Tokyo-Kyoto-Hiroshima itinerary I may decide to also spend some time in Osaka. In that case I can use my base fare ticket from Kyoto to Shin-Osaka, and proceed to Hiroshima by Shinkansen from Shin-Osaka later.

If you are inside ticket gates when the validity period of your ticket expires, the same rules as those of the Japan Rail Pass apply: your ticket remains valid until you exit the ticket gates at a station (regardless of whether it is your final destination).

Valid route

In some cases there may be several possible routes between your departure and arrival stations, and you will need to choose the one on which your base fare ticket will be valid. For example for travel between Nara and Hiroshima, it is possible to go from Nara to Shin-Osaka (via Tennoji) and on to Hiroshima by Shinkansen, or from Nara to Kyoto and on to Hiroshima. The valid route is printed on the ticket.

Exception: Shinkansen and ordinary lines running in parallel

When Shinkansen and ordinary JR lines run in parallel, a base fare ticket is equally valid on both, regardless of what is written on it. It also allows changing between one and the other at the stations where they meet, subject to the no-backtracking rule. This is why, for example, during my trip from Tokyo to Hiroshima I can use ordinary lines between Kyoto and Shin-Osaka, even if my base fare ticket says Shinkansen. The sections where this is possible are

  • Between Tokyo and Shin-Shimonoseki (Tokaido/Sanyo Shinkansen).
  • Between Tokyo and Morioka (Tohoku Shinkansen).
  • Between Hakata and Shin-Yatsushiro and between Sendai and Kagoshima-Chuo (Kyushu Shinkansen).
  • Between Tokyo and Niigata (Joetsu Shinkansen).
  • Between Fukushima and Shinjo (Yamagata Shinkansen) and between Morioka and Akita (Akita Shinkansen), because there the Shinkansen and ordinary trains actually use the same tracks.

Note in particular that even though Shinkansen and ordinary JR lines do run in parallel between Shin-Shimonoseki and Hakata, they are not "compatible", and it is imperative to follow the route displayed on the ticket. In other cases (between Morioka and Shin-Hakodate-Hokuto, between Shin-Yatsushiro and Sendai, and between Takasaki and Kanazawa) there are no ordinary JR lines running in parallel with the Shinkansen.

No backtracking

For a base fare ticket to be valid, travel must proceed always in the same direction, with no backtracking.

Suppose, for example, that I am in Kyoto, and want to go to Fukuoka (Hakata station) with a stopover in Hiroshima to visit Miyajima island. I plan to use the Shinkansen from Kyoto to Hiroshima, and again from Hiroshima to Hakata. After exiting the Shinkansen gates at Hiroshima and perhaps eating a good okonomiyaki somewhere near the station, I inadvertently use my base fare ticket to go from Hiroshima to Miyajimaguchi station.

Since Miyajimaguchi is to the west of Hiroshima, this is allowed. However, then I must proceed west from Miyajimaguchi: if I try to go back to Hiroshima, my ticket will be rejected, and it will also no longer be valid for my Shinkansen travel from Hiroshima to Hakata. In that case, I can either get a refund for the unused section (between Miyajimaguchi and Hakata) and buy new tickets, or proceed west from Miyajimaguchi to Tokuyama on local trains and then on the Shinkansen from Tokuyama to Hakata.

No stopover permitted inside city zones

If I buy a base fare ticket from Kyoto to Tokyo, what I really get is a ticket from the Kyoto city zone to the Tokyo city zone. In that case, I can enter at any station in the Kyoto city zone, and exit at any station in the Tokyo city zone. However, no stopover is permitted in either city zone.

If I enter at a station in the Kyoto city zone and exit at another, my ticket will become invalid. However, in that case I can get it back by paying the normal fare between the two stations. Likewise, if I exit at any station in the Tokyo city zone, it will be considered to be my final destination, and my ticket will not be returned (and I cannot get it back if I actually intended to go to some other station).

There are eleven such city zones: in Sapporo, Sendai, Tokyo, Yokohama, Nagoya, Kyoto, Osaka, Kobe, Hiroshima, Kitakyushu, and Fukuoka. Stopovers are permitted (subject to the no-backtracking rule) inside city zones encountered along the way, such as Nagoya or Yokohama during a trip from Kyoto to Tokyo.

Exceptions: in Osaka and Kobe

In Osaka, the JR stations of Osaka and Kitashinchi are connected by a walkway. Walking between them is permitted on a base fare ticket with departure or arrival in the Osaka city zone, even though it requires exiting the ticket gates (Hyperdia gets this one wrong). However, the transfer must be made within one day (i.e., one must exit one station and enter the other on the same day), and doing this is not permitted in any other circumstance.

In Kobe, the Shinkansen station of Shin-Kobe is not linked to the other stations of the city zone by JR lines, and thus it is necessary to exit the ticket gates to transfer between the Shinkansen and ordinary lines. This is permitted on a base fare ticket with departure or arrival in the Kobe city zone, but only to or from the stations of Sannomiya, Motomachi, Kobe, and Shin-Nagata (Hyperdia gets this one wrong too). As in Osaka, the transfer must be made within one day, and doing this is not permitted in any other circumstance. Also, if one uses the Kobe subway to go to Shin-Kobe, the subway fare must of course be paid separately.

  • 2
    Trivia: the longest trip on a single base fare ticket that I can find is between Wakkanai (at the northern tip of Hokkaido) and Shibushi in southern Miyazaki prefecture. The distance is 3235.5 kilometers, so a base fare ticket will be valid for 17 days. It costs 30,450 yen. – fkraiem Apr 16 '16 at 17:48
  • 1
    Sorry, 18 days, not 17. – fkraiem Apr 16 '16 at 17:54
  • A clarification question: so I'm allowed to depart from the "direct" track? Say I have a base fare ticket from Kyoto to Hakata. I take the Sanyo Shinkansen to Okayama, then go for a detour to Matsuyama, then from Matsuyama take the ferry to Hiroshima, where I continue to Hakata. Will this be OK, provided I pay for all limited express fares (and the ferry)? – xuq01 Aug 8 '18 at 5:34
  • OK, seems not... Looks I'd need to buy Kyoto to Matsuyama, then Hiroshima to Fukuoka. – xuq01 Aug 8 '18 at 13:04
  • @xuq01 You are not allowed to depart from the route you paid for, which is written on your ticket. So if you paid for the "direct" route (by which you probably mean the Tokaido/Sanyo Shinkansen), you can't depart from it. If you want to go from Kyoto to Matsuyama, you must pay Kyoto to Matsuyama, and then you have no valid rail route to Hakata that does not involve backtracking, so no, you can't do that on a single ticket. – fkraiem Aug 8 '18 at 15:23

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