What are some of the best museums in Japan?

I haven’t visited many museums in Japan, but the Izu Teddy Bear Museum in Itō is one of the best I’ve been to. It just has so much charm and sense of childhood nostalgia with its huge variety of teddy bear exhibits. There are also some Ghibli characters on display, including a huge Catbus that you can go inside of. Love the teddy bear carnival and the Hina bear display.

The parasite museum in Meguro is interesting. But go after lunch.

The Higashiyama Kaii museum in Nagano City.

Miraikan was great when I went a few years back:

https://www.miraikan.jst.go.jp/en/

The Railway Museum, which I've never visited though, is one of the most famous museums in Japan. It is located in Saitama Pref. You can get there in a few minutes by train from Omiya station. There are variety of attractions that anyone can enjoy regardless of ages. First, 42 real mock-up trains including Shinkansen and Steam Locomotives, are exhibited at the site. Second, you can experience the field of railway company through simulator and workshop. Third, you can learn the history of how Japanese railway system have developed from many points of views such as science. Not only adults but also children can enjoy through a day. When you are tired walking around in the museum, you can rest at the cafes and restaurants. At the restaurant, ekiben(a special lunch box that can only available at the station) can be bought.

Highly recommend.

The dinosaur museum in Katsuyama, Fukui is a delight. It's a bit tricky to get to but worth it.

The sand sculpture museum in Tottori is also very interesting and exhibits change periodically so you get a new experience every time.

The kimono museum in Kawaguchi-ko on the north side of Mt. Fuji is very nice as well.

Most museums here are fusty,dusty,hands-off antiquated displays of dilapidated mannequins and badly labelled rocks.

Funnel some of the town hall moolah into making these places into interactive,child-friendly spaces,and then we're talking.

Hiroshima peace museum.

Otsuka Museum of Art in Naruto Tokushima :

https://o-museum.or.jp/en/

https://www.pref.tokushima.lg.jp/en/japanese/tourism/spot/ootsuka

Absolutely stunning and definitely worth a visit! !

Otsuka Museum of Art in Naruto Tokushima 

I second that. While there, staying on Naoshima art island next door at the Bennesse Museum Hotel is also a great experience.

Tokyo's National Museum of Nature and Science located in Ueno Park, is a very interesting museum for young people . . . has the skeleton of a Pleiosaur . . . and other exhibits

National Museum of Nature and Science | Travel Japan (Japan National Tourism Organization)