Rural area in japan

We are a couple with a 5 month old baby. we are planing to visit Japan for two weeks on April. We would like to get to Tokyo and Kyoto, but also to stay on rural area and small villages. Do you have any recommendation about beautiful rural area around those cities (it could be few hours long by train or bus too).
Thank you very much

Hakone is nice and sort of on the way between the two.
http://traveljapanblog.com/wordpress/tag/hakone/

Koyasan is also excellent as a one nighter away from Kyoto. When I stayed at Fudoin there was a couple with their young child at the same place having a great time.
http://traveljapanblog.com/wordpress/tag/koyasan-%E9%AB%98%E9%87%8E%E5...

How about islands?
http://ritokei.com/land
http://www.geocities.jp/warera_tikyujin/island_japan/island_japan.html
http://japan-web-magazine.com/japanese/island/index.html

Some of the rural areas can be challenging if you dont speak Japanese, so it is good to go to one which is touristy even if it is mainly local tourists.

Tsumago and Magome would be worth considering, and so would Takayama and in particular Shirakawa-go. Each are pretty accessible via Nagoya which is on the shinkansen line between Tokyo and Kyoto. The train trip from Nagoya to Takayama is spectacular, then you bus from Takayama to Shirakawa-go. Takayama and Shirakawa have better english facilities. But Tsumago and Magome have their own charms, that is a train ride from Nagoya then a bus or taxi to Tsumago. I didnt stay in town, but I understand that the ryokan/pension stays in Tsumago are a lot of fun.

If it is more just seeing some foresty areas, then I really like Enoshima and Kamakura (near Tokyo), and near Kyoto I like Nara and Uji.

You may refer to the website below regarding the trip around Chubu district.
http://tourguides.nagoya/en/index.html

You can go pretty much anywhere in Japan in a "few hours" from Tokyo or Kyoto, including to Hokkaido or Okinawa if you allow transportation by plane.

My biggest problem when people ask which rural places to visit in Japan goes like this - how long is a piece of string.

It really depends on how much you want to travel - specifically with a little one. As mentioned by someone above - Japanese ability can be important if you need to source some harder to get things in rural areas.

As you are heading from Tokyo to Kyoto - I'm guessing the Kanto, Chubu and Kansai regions are probably your best bet. A 2 or 3 day sojourn is probably your best bet.

The Magome/Tsumago visit is a nice one. I find that the Fujiwara in Tsumago is a nice place to stay.

Another option is visiting Takayama and also staying in a Gassho hut in Shirakawagoe along with visiting Furukawa.

If you really want to get off the beaten track - the Kii-Peninsula is a fantastic place to visit.

The Azu Peninsula which is close to Tokyo is also a nice place to visit and has reasonably good transport links (apart from the west coast)

The Noto Peninsula is probably the most rural area on Honshu but really needs a hire car to do it justice.

I also visited Iiyama (Nagano prefecture) last year and found it beautiful - but once again I also used a hire car in this area.

I've also got a list of 20+ more places to suggest but it really depends on how much you want to travel, for how long and what interests you....

You might want to rethink things. There are plenty of pleasantly non-urban areas less than an hour from Tokyo on the train as you get closer to the mountains. They feel a lot more rural but civilisation is only a regular and reliable train ride away.

The middle of nowhere or a tiny village is a risk with a 5 month old if you speak Japanese, considerably more so if you don't, particularly as Asian tummy bugs/wildlife and small Westerners can be a bad mix. Urban A&E doctors speak English. In rural areas, you'll be lucky to find anyone who does, and local medical facilities may be limited.

At the very least, load up you mobile with credit. In most cases it will cost a lot for you to call someone on roaming, and almost as much for them to call you, so credit runs out quickly. And double up on mobile devices.

In general, Western medical insurance emergency helplines are poor/useless, and that's in urban areas where they have subcontracted call centres.

Might be wise to save the Robinson Crusoe stuff until the little one is a bit older.

I am going to recommend Chichibu, which is near Tokyo. If you take the Yamanote Line train to Ikebukuro, there is a private train line that goes directly to Chichibu.

The tourism office, which is on the right side outside of the Seibu-Chichibu station, will usually has someone who speaks English. The town has lots of festivals, and has a pilgrimage route that you can go on.

If you are going at the end of April, you should go see the Moss Phlox garden at Hitsujiyama Park. Here is their tourism page:

http://www.seibu-group.co.jp/railways/tourist/english/sightseeing/chic...

The second place would be Takayama and Shirakawa-go, especially if you can go during the spring festival in mid April.

http://www.japan-guide.com/e/e5909.html
http://www.japan-guide.com/e/e5950.html

The third place I would suggest would be the Hot Springs Beach resort of Atami, which is near Hakone. There is a spring Fireworks display on April 9th this year. More links:

https://shizuokatourism.com/atami-city/
http://www.atamispa.com/atami_ex/english/sightseeing/index.htm

All of these places have some special tourism appeal, so there are things to do in these smaller cities, and if you have any troubles, you should find people that can speak English to help you.

I hope this helps.

Kurama and Ohara, north of Kyoto city, is only one hour distance. Good for a baby.

http://www.japan-guide.com/e/e3932.html
http://www.japan-guide.com/e/e3933.html