This itinerary includes Kyoto, Osaka, Hiroshima, Miyajima and North part of Kyushu (Hakata, Nagasaki, Aso and Beppu). This starts from Tokyo and your Japan Rail pass will be started to use from Tokyo station. You may start this itinerary from Shinagawa station, if you arrive at Haneda airport early morning. And of course, you can start this itinerary from Osaka or Kansai airport too. Osaka and Kansai airport are much closer to Kyoto than Tokyo. If you start this itinerary from Osaka, the itinerary is more smooth and easier.
06:26am Depart from Tokyo station by Tokaido Shinkansen Hikari 501.
09:16am Arrive at Kyoto station. After arrival, enjoy exploring in Kyoto.
*Hikari departs at Tokyo station every 30 minutes. If you want to depart a bit later, you can take later Hikari. If you arrive at Narita or Haneda early morning, you can transfer to Kyoto on the arrival day. If you need to check the timetable of Shinkansen, please check JR Central timetable.
Overnight in Kyoto
Half day free in Kyoto and transfer to Osaka by Shin-Kaisoku (新快速=Special Rapid service). After arrive at Osaka, enjoy sightseeing and shopping in downtown Osaka
Overnight in Osaka
*If you are not interested in Osaka or prefer to stay in Kyoto, you can extend to stay in Kyoto instead of Osaka. Kyoto is only 30 minutes away from Osaka by Local train Shin-Kaisoku (新快速=Special Rapid service), 10 minutes away from Shin-Osaka by Shinkansen.
Catch the local train to Shin-Osaka. It takes only 5 minutes from Osaka.
07:20am Depart from Shin-Osaka station by Sanyo Shinkansen Hikari 545.
09:16am Arrive at Hakata station. After arrival, enjoy exploring in Hakata.
I recommend to go to Dazaifu Tenmangu shrine when you stay in Hakata. And also Hakata give you casual supper experience at Yatai (屋台=Food stalls). You can enjoy many kinds of Japanese comfort food there.
Overnight in Hakata (Fukuoka)
07:54am Depart from Hakata station by Limited express Kamome 7.
09:50am Arrive at Nagasaki station. After arrival, enjoy exploring in Nagasaki.
Overnight in Nagasaki
06:00am Depart from Nagasaki station by Limited express Kamome 2.
07:31am Arrive at Shin-Tosu station. After arrival, transfer to Kyushu Shinkansen.
07:50am Depart from Shin-Tosu station by Kyushu Shinkansen Tsubame 331.
08:26am Arrive at Kumamoto station. After arrival, transfer to Limited express Kyushu Odan Tokkyu (=Trans-Kyushu Limited express).
08:35am Depart from Kumamoto station by Limited express Kyushu Odan Tokkyu 2.
09:44am Arrive at Aso station. After arrival, take a local bus to one of very popular active volcano, Mt. Aso.
*The bus to Mt. Aso depart once every one to two hours. The fare is 730 yen for one way to Aso Nishi station. Aso Nishi station is the depart point to take Gondola. The gondola fare is another 1,000 yen for round trip.
16:28pm Depart from Aso station by Limited express Kyushu Odan Tokkyu 6.
17:39pm Arrive at Beppu station. Stay at most famous hot springs resort in Kyushu.
Overnight in Beppu
Enjoy half day sightseeing in Beppu
12:53pm Depart from Beppu station by Limited express Sonic 32.
14:03pm Arrive at Kokura station. After arrival, transfer to Sanyo Shinkansen.
14:22pm Depart from Kokura station by Sanyo Shinkansen Sakura 566.
15:09pm Arrive at Hiroshima. After arrive at Hiroshima, enjoy sightseeing in downtown Hiroshima.
Overnight in Hiroshima
Enjoy full day sightseeing in Miyajima. Please refer the post, How to get Miyajima, about access from Hiroshima.
After sightseeing, take Sanyo Shinkansen to Okayama.
21:15pm Depart from Hiroshima station by Sanyo Shinkansen Sakura 580.
21:57pm Arrive at Okayama station
22:33pm Take Sunrise Seto/Izumo at Okayama station. Overnight in the train.
*As far as you don’t get off overnight train, Japan Rail Pass 7 days cover your basic fare and express surcharge. If you don’t exit the station, Japan Rail Pass still cover basic fare.
07:08am Arrive at Tokyo station.
If you don’t exit the station, you can continue your trip. Japan Rail Pass cover the basic fare. But it does not cover surcharge. So if you go to Narita airport, you can take Rapid Airport Narita with no extra charge.