This itinerary includes many popular spots throughout Japan in 14 days. This itinerary starts from Tokyo. But if you want to start from Osaka, you can start from Day 11 to Day 14, and then start from Day 1 to Day10. Actually 14 days in not enough to see all popular spots in Japan. I include Hokkaido in this itinerary. But it does not include Shiretoko because of not enough time. I could not include south part of Kyushu, Hakone and Mt. Fuji either. If you can give up Tohoku part, you can get more time in Hokkaido. Of course you can go to Shiretoko.
Anyway this is a sample. I hope this sample itinerary help you When you make your own plan.
08:08am Depart from Tokyo by Tohoku Shinkansen Max Yamabiko 127
09:01am Arrive at Utsunomiya station
09:12am Depart from Utsunomiya station by Nikko line local train
09:54am Arrive at Nikko station. After arrival, enjoy exploring in UNESCO World Heritage site, Nikko
14:20pm Depart from Nikko station by Nikko line local train
15:01pm Arrive at Utsunomiya station
15:59pm Depart from Utsunomiya station by Yamagata Shinkansen Tsubasa 143
18:00pm Arrive at Yamagata
*You can get Nikko from Shinjuku directly by Limited Express Nikko. But this express train goes on Tobu line. Japan Rail Pass does not cover this section. If you need more info, please refer Limited Express Nikko and Kinugawa.
*You can go to Zao Hot Springs after arrival at Yamagata. I choose only major cities to stay in this itinerary because you can find the accommodation very easily. But you can skip Yamagata and go straight to Zao. The last bus depart from Yamagata station to Zao at 18:40 and arrive at Zao at 19:17. (2011 summer timetable) Zao hot springs is a nice spa resort.
Overnight in Yamagata
07:40am Depart from Yamagata station by Yamako bus
08:17am Arrive at Zao hot springs
Zao Ropeway start to operate at 08:30am. You can enjoy the fresh air and easy trekking at the summit. You can enjoy it for 1.5 hour.
10:10am Depart from Zao hot springs by Yamako bus
11:07am Arrive at Zao Kattasancho (Zao the summit of Katta mountain. It is known as “Okama”.)
Okama is a lava lake. You cannot access this spot in winter time. There is only one restaurant there. So it is very busy in lunch time. If you have a plan to have a lunch there, please make sure your schedule.
13:00pm Depart from Zao Kattasancho by Yamako bus
14:40pm Arrive at Yamagata station
*The extra cost to get to Zao is the following:
Yamako bus from Yamagata station to Zao hot springs — 980yen one way
Yamako bus from Zao hot springs to Zao Kattasancho — 1430yen one way
Yamako bus from Zao Kattasancho to Yamagata station — 1900yen one way
Zao Ropeway to the summit — 2500yen round trip
15:43pm Depart from Yamagata station by Senzan line local train
15:59pm arrive at Yamadera station
Yamadera means the mountain temple. There are several temples. Most well-known haiku poet Basho Matsuo wrote one of his famous haiku there. You can skip here if you want to arrive at Sendai earlier.
17:59 Depart from Yamadera station by Senzan line local train
18:59 Arrive at Sendai
Overnight in Sendai
08:59am Depart from Sendai station by Senseki line local train
09:35am Arrive at Matsushima Kaigan station
*The pier is 5 minutes away from the station
10:00am Depart from Matsushima Kaigan pier by Matsuhima bay cruise
10:50am Arrive at Matsushima Kaigan pier
*The fare for Matsushima bay cruise is 1400yen per person
*You can enjoy easy hike up to Ogitani. The trail head is 10 minutes away from the station. It takes only 10 minutes hike up to the view point. Enjoy the panorama view of Matsushima.
You can enjoy a fresh seafood lunch here at Matsushima Sakana Ichiba (Matsushima fish market — Japanese website) after sightseeing at Matsushima. You may have a seafood lunch around 1000yen. Of course you can go back to Sendai.
12:34pm Depart from Matsushima Kaigan station by Senseki line local train
12:58pm Arrive at Sendai station
13:42pm Depart from Sendai station by Tohoku Shinkansen Yamabiko 59
14:14pm Arrive at Ichinoseki station
14:37pm Depart from Ichonoseki station by Tohoku line local train
14:45pm Arrive at Hiramizumi station
You can enjoy the newest UNESCO World Heritage site, Hiraizumi. The most famous spot in Hiraizumi is Chusonji temple. It is 25 minutes (1.6km) away from Hiraizumi station. The admission is 800yen per person. (English website)
17:39pm Depart from Hiraizumi station by Tohoku line local train
18:10pm Arrive at Kitakami station
18:33pm Depart from Kitakami station by Tohoku Shinkansen Yamabiko 67
18:52pm Arrive at Morioka station
(Dinner break at Morioka)
20:26pm Depart from Morioka station by Tohoku Shinkansen Hayate 37
21:28pm Arrive at Shin-Aomori station
21:38pm Depart from Shin-Aomori station by Local train
21:44pm Arrive at Aomori station
22:42pm Depart from Aomori by overnight express train Hamanasu
Overnight in the train
06:07am Arrive at Sapporo station
Full day free in Sappro. You have several choice, staying in Sapporo, half day trip to Otaru, full day trip to Furano, or you can go even Kushiro marsh. You can get some information about Furano at Furano Lavender Express / Furano Koyo Express. If you are looking for day trip to Kushiro from Sapporo, please refer Kushiro Shitsugen Norokko train.
Overnight in Sapporo
*You can extend to stay in Sapporo instead of Hakodate. If you don’t need to stay in Hakodate, you can take Super Hokuto 16 (Sapporo 14:52 – Hakodate 18:09).
19:18 Depart from Hakodate station by Super Hakucho 98
21:22 Arrive at Aomori station
Overnight in Aomori
*Before you depart from the hotel, ask to store your luggage to the hotel. Because you will walk along Oirase gorge. It is short hike, but you cannot carry your luggage.
07:50am Leave Aomori station by JR Tohoku Bus Mizuumi 2
10:35am Arrive at Towadako station
Enjoy Lake Towada
12:30pm Depart from Towadako station by JR Tohoku Bus Mizuumi 7
12:56pm Arrive at Kumoi no Taki bus stop
Enjoy walking from Kumoi no Taki to Ishigedo
14:35pm Depart from Ishigedo bus stop by JR Tohoku Bus Mizuumi 9
17:04pm Arrive at Aomori station
*Don’t forget to pick up your luggage at the hotel.
17:51pm Depart from Aomori station by Super Hakucho 40
17:56pm Arrive at Shin-Aomori station
18:14pm Depart from Shin-Aomori station by Tohoku Shinkansen Hayabusa 6
21:24pm Arrive at Tokyo station
22:00pm Depart from Tokyo station by Overnight train Sunrise Seto/Izumo.
Overnight in the train
06:27am Arrive at Okayama station
07:16am Depart from Oakayam by Sanyo Shinkansen Hikari 541
09:13am Arrive at Hakata station
09:55am Depart from Hakata station by Limited Express Kamome 13.
11:48am Arrive at Nagasaki station.
After arrival, enjoy exploring 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.
09:43am Arrive at Aso station. After arrival, take a local bus to one of very popular active volcano, Mt. Aso.
10:00am The bus to Mt. Aso depart from Aso station.
10:40am Arrive in Mt. Aso West (Gondola station). The bus fare is 730 yen for one way to Aso Nishi station. The gondola fare is another 1,000 yen for round trip.
13:05pm Depart from Mt Aso West by bus to Kusasenri/Mt. Aso Museum. The bus fare is 140 yen.
13:10pm Arrive at Kusasenri/Mt. Aso Museum.
15:40pm The bus depart to Aso station from Kusasenri/Mt. Aso Museum. The bus fare is 670 yen.
*You can spend your time for the gondola only. In case of that, the bus leave rfom Mt. Aso West at 15:35pm.
*Unfortunately the bus company (Kyushu Sanko Bus Line) does not have any English website. But the gondola company Mt. Aso Ropeway has English site.
16:13pm Depart from Aso station by Trans-Kyushu Limited express 6.
18:13pm 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.
16:15pm Depart from Hiroshima station by Sanyo Shinkansen Sakura 568.
17:44pm Arrive at Shin-Osaka station
17:50pm Depart from Shin-Osaka station by Tokaido Shinkansen Kodama 478
18:05pm Arrive at Kyoto
Overnight in Kyoto
Full day for exploring in Kyoto
Overnight in Kyoto
Overnight in Kanazawa
08:45am Depart from Kanazawa for Shirakawa-go by Nohi Bus.
Reservation Required!!! Don’t forget to make a reservation. This bus is not included in Japan Rail Pass. The bus fare 1,800yen.
10:00am Arrive at Shirakawa-go
*If you need more information about access to Shikawago, please refer one of my posts, How to get Shirakawa-go.
Enjoy sightseeing UNESCO world heritage site Shirakawa-go.
*Reservation Required!!! Don’t forget to make a reservation. This bus is not included in Japan Rail Pass. The bus fare 2,400yen.
17:20pm Depart from Shirakawa-go for Kanazawa by Nohi Bus
18:10pm Arrive at Takayama
Overnight in Takayama
Eenjoy sightseeing in very traditional Japanese town, Takayama.
18:45pm Depart from Takayama by “Wide View Hida 20”
21:00pm Arrive at Nagoya
21:27pm Depart from Nagoya by Tokaido Shinakansen “Hikari 534”
23:26pm Arrive at Tokyo