Get a 21 day JR pass. You will need to plan ahead to do this, because your paperwork will be sent to you via mail. You won’t want to do this last minute.
Day 1: Arrive in Tokyo
Once you get to Tokyo, pick up your JR pass at the airport. You can then take the monorail and JR trains (subway lines will cost you extra, but when you get tired of walking you will likely end up taking them) to get to your accommodations. Just show your pass to the staff at station entrances when entering JR stations. Google Maps can help you find your way via trains and by foot if you pick up a pocket wifi at the airport as well, or if you have international data.
I would suggest taking a rest today. Walk around near your Tokyo accommodation, and eat some good food. (But avoid scam restaurants like this one!).
Day 2: Tokyo DisneySea
If you are a Disney fan, take your second day in Tokyo to visit a park that’s only in Japan, Tokyo DisneySea! There are some totally unique park environments here, and some familiar rides as well, including Indian Jones and the Tower of Terror. There are also some interesting food combinations/interpretations here, including Mexican food with a Japanese twist. The park isn’t huge, so it is likely that you will spend around a half day here.
If you end up having some time to explore other parts of Tokyo in the second half of your day, consider shopping in Harajuku, or checking out the anime capital in Akihabara. The JR train will get you everywhere that you need to go.
Day 3: Exploring the City
Spend the day seeing some of the different areas of Tokyo. I have mentioned a couple above, but some other neat locations are Meiji shrine and the park surrounding the temple. There is also a beautiful garden in Shinjuku that is a great place to spend an hour or so, and escape the crowds for a bit.
Day 4: Journey to Mt. Fuji
Mt. Fuji’s hiking season is from early July to early September; it is illegal and extremely dangerous to attempt the summit outside of the hiking season. So, if you plan on including this in your trip, make sure you plan accordingly. I would also suggest that you try to get out on the trail during the very first week of the season, as it will only get more and more busy once school lets out.
In order to get there, take a bus from Tokyo to Mt. Fuji’s Fifth Station; note that you should plan on buying your tickets for this ahead of time so that you are guaranteed a seat. You can do this online here. The ride takes around 2.5 hours and is on a mountain road, so take some motion sickness medicine if you struggle with that.
The fifth station is a pretty big tourist stop, so it can be quite busy there, but it is also a great area for resources for those of you trying to travel light. They have rain gear that you can rent, along with some other equipment options if you need trekking poles; never rent hiking boots, as you NEED to hike in shoes that you have already broken in. There are also a bunch of options for a hot meal before you set off.
When we did this hike, we decided to just make it to the hut where we were staying for the night on the first day, and since this was the highest hut on the mountain where you can stay the night (Goraikokan), I think that this worked really well. Although, be aware that this is a popular place to stay, and you will need to be proactive about reserving yourself a spot there. Also, Goraikokan is at a relatively high altitude for most of us, so be sure to plan ahead to prevent altitude sickness one way or another (here are some tips).
Day 5: Summit Mt. Fuji and Return to Tokyo
If you are a strong hiker, summiting from Goraikokan will most likely take longer than you are expecting, because there is a good chance that you will be forced to queue up near the summit. When we went, I think we spent about an hour in line, and we were lucky that it had cleared up a bit when we started down, because there were times that the line was in both directions.
Depending on how early you get to the top, how much energy you have, and when your bus home leaves the 5th station, you may want to walk the trail that circles the summit. Otherwise, enjoy the top and then start the long hike downhill. This part of the trek destroyed my legs, whereas, I was just fine hiking up. Be ready for a long, steep walk down the mountain.
We caught the bus back to Tokyo once we got down, and then we basically just ate dinner and fell asleep (you probably won’t sleep well at the mountain hut, unless you enjoy sleeping shoulder to shoulder with strangers).
Suggestion for accommodations (budget): Khaosan Tokyo Samurai Capsule – This is the first capsule hostel/hotel that I have ever stayed in, and I wish all hostels were like this! You had your own space, and the staff here are great!
Day 6: Traveling to Kyoto
After our adventure on Mt. Fuji, and a night’s rest in Tokyo, we hopped right on the Shinkansen (or bullet train) to Kyoto (my favorite city in Japan!!). It takes about 3.5 hours to make it from Tokyo to Kyoto, and that’s not including the city trains you may need to take.
This may be a an all day affair, depending on when you leave, but if you get to Kyoto and have some time, try walking around the Gion area. The architecture and atmosphere in this area is absolutely beautiful, and there are some beautiful canals that you can walk along. Plus, plenty of food.
Day 7: Kyoto
Take the train over to Inari-Jinja (http://www.japan-guide.com/e/e3915.html). This shrine here is one of the coolest locations in Kyoto, and will be familiar if you ever watched Memoirs of a Geisha. Here, you can hike through tunnels of torii gates, and if you are so inclined (which I highly recommend), you can hike up Mt Inari to the shrine at the top of the mountain. The trail to the summit is really unique, and it is a great place to experience some Japanese forests (which surprisingly, you don’t get much of on Mt. Fuji).
After Inari, head back over to the Gion area. There are plenty of shrines to explore there, but I would suggest Kennin-ji, the oldest zen shrine in Kyoto, and where you can see a HUGE dragon mural. Afterwards, consider catching a performance at Gion Corner, which has a nice little show with six different traditional Japanese preforming arts, including Geisha dances.
If you didn’t have the chance yet to enjoy the canals in Gion by night, please do so tonight. I absolutely love this area.
Day 8: Kyoto
Take today to visit some of the other shrines/sites in Kyoto that you haven’t seen yet.
You may be tempted to visit the Bamboo Forest, which is in a ton of pictures and blogs, but I thought that it was too busy and the forest was so small that it really wasn’t worth visiting. The area surrounding the forest is pretty nice, however, so if you really feel the need to check it out, you can spend some time in the area.
I would suggest that you brave the crowds to check out Kinkaku-ji, or the golden pavilion, however. It is a really unique spot, so I think it is well worth the lines and hordes of people. But if neither of these is on your list, there is plenty to do and see in Kyoto; I think you could spend a full week in this city and still not run out of things to do.
Day 9: Hiroshima and Miyajima
Take the shinkansen to Hiroshima; it takes about 2.5 hours, but it is likely that you will need to transfer, so give yourself some time by getting an early start. Once you are in the city, be sure to visit the Atomic Bomb Dome, the Peace Park, and Hiroshima Peace Memorial Museum. This is absolutely one of the most moving places that I have ever been.
After a sobering afternoon, take the train over to the Miyajima ferry terminal. It is a short ride over to the island, and is covered by the JR pass. If you get there before it closes, check out the Itsukushima Shrine, which has a massive torii gate in the ocean. It is a wonderful place to unwind. If you get in too late for that, feel free to stroll around the town in Miyajima. Lots of things will close early, but the views are beautiful, and there are also deer that mingle among humans here, so it is a very cool place. Please don’t feed them anything though, especially things that aren’t edible (like maps… seriously, people feed them maps.).
Suggestion for accommodations: Hotel Sakuraya– this is a small bed and breakfast with traditional Japanese baths and a prime location on the shore.
Day 10: Miyajima
Sleep in, have a nice breakfast in town, and then take the gondola (or trail) up to the top of Mt. Misan. Not only are the views from the mountain absolutely stunning (you can see the ocean in both directions as well as the big island of Japan surrounding the island), but there is a complex of shrines on top of the mountain. These ancient buildings are home to a sacred fire, and are perched in some of the coolest spots just about anywhere. If you enjoy hiking, definitely take the trail down, because it is a great way to see the forest, as well as some famous anti-erosion landscape engineering. Specifically, there are dams and artificial waterfalls meant to prevent flooding and erosion on the island here, and they are all very sensitive to the nature of the surrounding forest.
For Part 2, head over here.