I understand OP author might not need this answer anymore, but others may. There is one just like MD TV show… It is located in Kyoto backstreets. It has an English menu where prices are higher. The category of that eatery style is called izakaya. There are numerous izakaya places n Tokyo and in Osaka, pretty much is a drink bar with some (few) meal options to help your alcohol intake sit well.
The restaurant in the series is supposedly set in Shinjuku’s Golden Gai, but there doesn’t really appear to be anything quite like it there.
However, this article (in Japanese) asserts that the actual inspiration was a real kushikatsu (fried stuff on a stick) joint called Yagura Kushikatsu in Tennoji, Osaka:
串カツ専門店 やぐら
+81 6-6714-7211
https://maps.app.goo.gl/YRbmLxHaS3rGkbFf6
The connection is a bit convoluted though. Like the series, Yagura’s regulars include taxi drivers, nightlife workers, and others up in the middle of the night. One of them was famous rakugo actor/singer Jakusaburō Katsura, who wrote a song about the restaurant called Yagura March (やぐら行進曲) in 1996, talking about a magical shop that opens at midnight with characters including those taxi drivers and a "Cinderella forgotten by time". Japanese manga artist Yaro Abe heard the song, liked the concept, and that’s how the Midnight Diner comic and later TV series were born.
However, Abe never visited the restaurant, so many details like the idea of not having a menu are not the same. Also, the original Yagura relocated from the original Kyobashi to Tennoji some time ago, and the new location is open during regular business hours, not in the middle of the night. Perhaps easier for tourists, but not quite so atmospheric.
For what it’s worth, in my student days I used to be a regular at a very Midnight Dinerish establishment in Shimokitazawa, Tokyo, which was open very late and where the menu consisted of whatever was on hand that day (the deep-fried river shrimp/kawaebi were to die for). However, the owner had a drinking problem, ran into trouble with some gentlemen in loud suits missing their pinky fingers, and had to leave town on short notice. Hope you’re doing OK, Kashihara-san…
Take it from one who first traveled to Japan over 50 years ago and has had
good fortune to return many times.. See my photo of Yodo River in Osaka below
The area of Shinjuku known as "Golden Gai" has about an 8 block labyrith of small
bar/cafe’s that in some cases only accomondate 8 to 10 people. Many of which are members only establishments. Other’s require a cover charge. Because of this unique area of Shinjuku it is inundated with tourist tours and spectators, so much so that it lost it’s true favor. Locals, no longer find it their favorite spot due to the character and popularity of such Netflick programs as "Midnight diner" that was once a well kept secret has gone "public" much to the chagrin of Tokyo’s inhabitants. Originality has been lost to tourist commeercialism and chain establishments selling pseudo originality in many
of the unique neighborhoods through out major metropolis of the globe.
I’m a fan of NHK World (which I get through Sky TV here in the UK). I regularly catch a show called “Document 72 Hours”, and they have covered several late night/all night eating places. Here are a couple of examples:
I also remember seeing one quite a while ago about an all night noodle place near the docks in Akita, but cannot find a link.
Unfortunately, I’m not familiar with Midnight Diner, so can’t say if any of these places are anything like the fictional diner in the show.
I know none of the places featured above are in Shinjuku, but I would be pretty certain that, if such places exist in provincial towns and cities, then they almost certainly exist in Tokyo as well.
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