3 weeks in Japan in June

Check out Japan-guide.com. Excellent website on all this Japan.

I second what Tammy said about Japan-guide.com.

If there is any way you can postpone your visit from the unpredictable weather of June (possibility of typhoons etc in addition to rain) to early November, or go earlier till maybe late April, you will enjoy your trip a lot more. Japan is my favorite country to visit, even it is in June.

Thank you for the responses so far. This is the only time we can go and we have our flights already. It will be the last three weeks in June.
Thanks

We were in Kyushu last June. It was very rainy (more than usual) but for us better than being there during the hotter months. Rainy season is fine if you are prepared for it.

I’ve spent time in Tokyo, too. I would recommend Kawogoe and Mito as places to visit from Tokyo. They are popular with Japanese tourists, but you will likely find fewer non-Japanese tourists there. (Kamakura and Nikko are firmly on the foreign tourist circuit, but also well worth the time.)

For getting into nature, look at the Lonely Planet Hiking Japan guide. I haven’t seen the most recent edition, but older editions have been good. Some hikes are intense, but others are more gentle. This won’t exactly be “off the beaten path” as hiking is popular in Japan, but it will still be an interesting side of Japanese culture that you won’t see if you just stay in the cities.

Have a great time.

Beginning of June or end of June? That can make a difference with regard to heat & humidity.

Early June would be my preference if going to Tokyo and central Japan. Later in June...since its your first trip to Japan, you're going to want to see/do stuff in/around Tokyo no matter how hot it is, so I'd probably tough it out for a few days (maybe a whole week if you're heat-tolerant) in/around Tokyo, then fly to Hokkaido (the large northern island). Hokkaido is absolutely lovely, with wonderful weather in mid-summer, when Tokyo and much of Japan is sweltering and (for me at least) pretty miserable (BTW, Hokkaido is where Japanese go to enjoy lovely summer weather without suffering in the heat). A lot will depend on your tolerance/comfort level in intense heat (I wouldn't be worried much about rain). We enjoyed a couple wonderful weeks in Hokkaido during late June, then flew back to Tokyo for a few days before flying home. The heat in Tokyo was brutal. Walking down the street, I'd stop every few meters when the doors to a shop with very strong air conditioning would open - I'd feel a whoosh of blissfully cold air rush out, I'd pause there to enjoy it for a couple seconds, then continue down the street hoping for another shop door to open soon.

I certainly would not go south. Kyoto is great but I'd think twice about a visit during the full heat of summer. If you live someplace where the heat & humidity is intense and you don't mind it, then I'd worry less about basic comfort. For me, as much as I love Japan, I've pretty much given up on visiting much of the country from late June to early September (I don't so well in the kind of heat you'll experience). Hokkaido is the fix for that - one of my favorite places.

Some thoughts - I answered another thread, hope it’s useful for your trip. (I lived in Tokyo decades ago for 7+ years, visited last in 2019.) Here are some ideas in case you missed this thread! https://community.ricksteves.com/travel-forum/beyond-europe/first-trip-to-japan-b5d2700e-ff90-4677-bca3-247b55606746.

Of all the things I suggested above, consider a visit to this onsen on the outskirts of Tokyo, totally worthwhile! Maenohara onsen (old Japanese hot springs) close to Tokyo, you can get a taxi from nearby subway station. I sent some Japanese friends there, they loved it! It's extraordinary. We bathed and then put on our Yukatas to sit in in the tetami mat dining room and look at the Japanese garden, a real treat! Unless you have tattoos... (not allowed in any onsens that I know.) https://www.tripadvisor.com/Attraction_Review-g1066446-d3387591-Reviews-Maenohara_Onsen_Sayano_Yudokoro-Itabashi_Tokyo_Tokyo_Prefecture_Kanto.html

The Hiking in Japan guide was very useful while we lived there, (we probably hiked 40 mountains) but I would take it with a grain of salt and investigate the destinations. Not all were as amazing as indicated! And also A Guide to Japanese Hot Springs, where I discovered by FAR my favorite hike - Sandogoya, a day-hike into a remote area with accommodation in the mountains of Nikko National Park but NOT that close to Nikko. I sent some young intrepid friends there, they managed without speaking Japanese and said it was absolutely the best place they visited in Japan. The inn with the actual hot springs was so grotty (30 years ago) we only ever stayed at the adjacent one, believe it or not I found the phone number. Yunoka Pension. 0288-62-2326. We were not sorry to skip the hot springs, the hike into & out of these mountains is delightful! (My data gathering was all pre-internet, who know there are probably details on line now to both these inns.)

I understand Koya-san is more crowded than it was decades ago but we loved it and stayed in a buddhist monastery. It's a remote mountain area with myriad Buddhist temples, here's a GREAT you tuber who talks about her visit overnight at a temple, (it was nice to listen to her fluently bi-lingual discussions.) One Forum member mentioned meeting someone else who had stayed in this Koya-san temple. https://www.youtube.com/watch?v=h0vk9JzDSxs.

I have not stayed here, but if I ever go back to Kyoto, it's top of my list of places to stay, and they have 'western' style rooms with some Japanese ambience but beds off the floor, not on the floor, which I know I could no longer tolerate.https://youtu.be/hS4d7i6Mr_E?si=lcY40cVEdacVw9Tw.

Hope you have a great trip! Of all my overseas travel, Japan is the one place I could return to again and again, so much to explore.