I spent a lengthy amount of time in Japan this past year, 2 months in September and I just got home from another two months March-May. I spent quite a bit of time in lesser-known areas and wanted to share some of my favorite spots if you are looking to experience Japan with fewer tourists. 

Some quick details about me:

• -I (18F) stayed mainly in hostels, with a $60-70 budget a day. I think I stayed in four or five hotels the entire trip.  
• -I speak an intermediate level of Japanese and can read the majority of menus, signs, etc.. without problem. This really came in handy when reading because when you get FAR in the countryside, there sometimes is no service AND no English translations/no English speakers. 
• -I visited 27 prefectures over a collective 108 days in Japan with the two trips.

Overall favorite prefectures:

• -Hokkaido: so much nature, incredible skiing, not touristy, SO much snow even into April. I bet this would be amazing to escape the July heat!
• -Aomori: there isn’t much to do in the city of Aomori, but taking a road trip an hour outside gets you to a lot of really amazing places (Takayama Inari Shrine, tsuru no maishashi bridge, Cape Tappi)
• -Fukuoka: I loved this place so much because I visited during full bloom of cherry blossoms. Truly a stunning sight. 
• -Fukui: arguably my #1 favourite. I think I noticed one other foreigner during my entire time there, and the attractions there are so unmatched. This prefecture is dinosaur-themed, with huge statues of dinosaurs outside Fukui station, since it has the most dino bones than any other part of Japan. 

Favorite foods:

• -Soup curry, Hokkaido (it will change your life if you’ve never had it)
• -The Full Full Hakata (a bakery in Fukuoka, truly the best in the country imo)
• -Okonomiyaki (of course, I loved the ones in Osaka)

Unique indoor attractions only in Japan that are totally worth it:

• -Art aquarium in Ginza, Tokyo
• -Nebuta Museum Wa Rasse, Aomori
• -Observation decks were my FAVORITE! Tokyo Skytree, JR T38 in Sapporo, and Fukuoka tower were my top 3. 

Places that you CANNOT MISS if you want to see real Japan (a bit of a long list):

• -Echizen Daibutsu, Fukui: it houses the largest inside statue of Buddha in Japan, and it took my breath away. The temple grounds are beautiful and you can get a bird’s eye view of Fukui from the pagoda. 
• -Lake Toya, Hokkaido: renting a car for this IS WORTH IT! It is a two hour drive from Sapporo. Toya is a volcanic caldera lake and the sights were, literally, some of the best I’ve seen in Japan. There is tons to do around the lake, and my day trip consisted of hiking, waterfalls, ropeway, Hokkaido milk gelato.
• -Mount Aso, Kumamoto: I did this with public transportation from Kumamoto city, but renting a car would save both time and a headache. Aso is an active volcano and while the hike to get up close to the volcano is closed (due to activity), you can get pretty close enough to it. Close enough to breathe in the volcano fumes and uncontrollably cough, along with everyone else there, for the next thirty minutes. Several hiking trails around it are open though, and a few lakes, and it is very pretty. I was there from about 10am-3pm and did three hikes, pet some horses, and got ice cream. 
• -Matsushima Bay, Miyagi: Known as one of the top 3 views in all of Japan, it is 260 small islands off the coast of Miyagi. I did the Oku-Matsushima trail, which is a 10km hike that takes you all around the area through bamboo forests, a cemetery, wetlands, unique rock formations, beaches, etc.. at the end it takes you up the mountain to get an incredible view of the bay. Such a cool hike and I literally did not see a single person during my time there. 
• -Michinoku coastal trail, Aomori: there is tons of info online, but if you have specific questions feel free to ask. It was a gorgeous hike along the ocean. 
• -Sakurajima, Kagoshima: an island right off Kagoshima with an active volcano. 
• Toyama: typically an over-looked destination, it has a ton of fun things to do that make a perfect day trip. Glass museum, castle, temples and I was there during a festival.

Lastly, just a few places I do NOT recommend:

• -Okayama: just, no. Personally, I found the town to be quite depressing and the locals to not be very nice. Okay for a day trip but there is literally nothing to see in the city other than the castle and the garden. Plus, the castle wasn’t anything special. 
• -Kyoto in the spring. I absolutely loved it in the fall, but the amount of tourists in the spring literally destroyed the experience for me (there was an astonishing amount of disrespectful foreigners). Please consider visiting less popular destinations that still have the same charm as Kyoto during March/April. 
• -Tokyo DisneySea: It is significantly smaller than Disneyland but in my opinion not as fun. Sure, it's the only DisneySea in the world, but there really wasn’t anything crazy special about it. If you’re a die-hard Disney fan, then 100% sure, but I am a “go once for the experience” type girl. 

I hope this inspires any Japan travelers to get to know the lesser-known destinations 🙂 the golden route is beautiful but I would take these destinations over Osaka and Kyoto any day! (obviously you can't miss Tokyo).