If you will be traveling by train this summer, and want to spend as little as possible, or just want to take the scenic route, it's time to start thinking about your your plans. By far the cheapest way to travel during the holiday seasons is the Youth 18 Ticket (Seishun Jyuhachi Kippu). It costs ¥11500 for 5 non-consecutive days on any regular JR train in Japan. It's not good on the Shinkansen, or Tokkyu (the fastest express) Trains, but if you used one of those, it wouldn't be scenic.
The most popular route during the Seishun 18 Kippu season, is the JR Tokaido line, connecting Tokyo with Nagoya, Osaka and Kyoto. For this route, I recommend the Moonlight Nagara. This train is by far the most popular train used by Seishun 18 Kippu holders, as it will take you from Tokyo to Kyoto or Osaka over night, in your own reserved seat, for only ¥2300.
The Moonlight Nagara has changed a little bit since list time I used it. In years past, the Moonlight Nagara Left Tokyo Station at around 11:30 (which meant that you had to pay for the first half hour before midnight), and arrived in Kyoto at around 9am the next morning. In addition to the Moonlight Nagara, there was a second train running only during the Seishun 18 Kippu season that was completely free seating, and left from Shinagawa Station at 11:45. This was great if you were unable to get a seat on the Moonlight Nagara, but it was incredibly crowded, and uncomfortable, and they didn't turn the lights off at night.
This year, they have bumped the Moonlight Nagara's departure time back to 11:45, and replaced the seasonal night train with a second seasonal Moonlight Nagara #91 which runs between 7/18 and 8/21. Both trains are now reserved seating, which I interpret as meaning that the #91 is the same type of train as the regular Moonlight Nagara, with individual high backed seats, and completely reserved seating. The #91 leaves from Shinagawa station at 11:55pm, which means you will only have to buy a ¥230 or so regular ticket, but probably you don't have to at all, since calculating the fare from Shinagawa to 12:00 will be too much hassle for the guy manning the gate in Kyoto.
To make a reservation for either Moonlight Nagara, you must go to a Midori no Madoguchi at most JR stations. It is recommended that you make your reservations as soon as the ticket window opens 30 days in advance. You can't make reservations earlier than that, and if you try later than that, it is unlikely you will get a seat. Occasionally some seats do open up, but it's best not to take you chances. Seat reservations on these two trains are free.
For exact routes of the Moonlight Nagara, or other trains, including night trains to Hokkaido and Kyushu, I recommend that you pick up a copy of the JTB 時刻表 (JTB Pocket Timetable), available at most bookstores in the travel section for ¥500. There are other time table books, but I have found the JTB version the most complete and easy to use. That is not to say the time table books are easy to use however. It will take some figuring out, and you should be able to read the Kanji of the places you will be passing through, as well as knowing where you will be going on a map.
For more information on the Seishun 18 Kippu, take a look at this article on Japan-Guide.com
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