If you want ‘fine dining’ in Michelin star type restaurants then we can’t really offer much advice (in Japan at least!). However, if you want interesting, tasty ('oishi' in Japanese), accessible and affordable food there is a wealth of options to choose from. You can either follow your eyes and nose (literally!) and/or use a guide like Michelin who award ‘bib gourmands’ to inexpensive restaurants offering well cooked food with quality ingredients all over the world including Japan.

Frankly, we have rarely found any food in Japan that wasn’t good quality and tasty regardless of where it was purchased – from a humble convenience store right up to a ‘banquet’ meal in a five star Onsen. In between there is a host of choices:

There are cheap fast food outlets (offering a limited choice of noodle and rice dishes) from chains like Sukiya and Yoshinoya or independents through ‘family’ restaurants with a table service and an enormous menu to more up market restaurants in a more refined environment where you will often be seated in a private booth separated from the other guests by sliding screens - a bell or buzzer is used to attract the attention of the wait staff.
Cheap & cheerful - that's Yoshinoya

In most cases menus are supplemented with colourful pictures of each dish or a model of each dish displayed in the window to give the customer an idea of what each dish is made up of – but not always!
You can see what you are getting even if you don't always know what it is!

It is very common in Japan for restaurants/eateries to concentrate on a single type of dish and occasionally with one or two options. So it is very useful to have a good idea of what these dish type are in advance and the most popular ones are:

Sushi – now popular in the west so needing little explanation

Tempura – seafood or vegetables (anything you can think of – lotus root is popular) flash fried in a wheat and rice flour batter

Ramen – also becoming popular in the west. While Ramen (or other noodle types like Soba and Udon) noodles are widely available it is all down to the quality of the broth and the freshness of the ingredients. The good ones are exceptional and you will often find long queues outside them at busy times. As they are often just simple bars it is common to make your selection and payment at a machine by the entrance and take a ticket to your seat

Okonomiyaki – basically egg pancakes with a mixture of meat and vegetables either cooked at a hot plate on the bar in front of you or finished off on a hot plate at your table. Usually accompanied by lashings of sauces, sometimes coming in a small bucket with a paintbrush to slather on your dish! Fantastic

Gyoza – small, ‘pot sticker’ dumplings filled with meat or vegetable mix. Quite often they are available on menus at other restaurants but in some cities, Utsonomiya – the ‘gyoza capital of Japan’ you will find restaurants selling only Gyoza

Yakitori – grilled meat on wooden skewers. Much like kebabs although the flavourings are different.

Kaiseki – Finally, the Japanese are very partial to meals made up of a large number of small and very different dishes. Incidentally the traditional Japanese breakfast is like this although most dishes are cold and pickled! Kaiseki style meals can be found from cheap chains (Washoku Sato is a good one) through middling restaurants and right up to very expensive, ‘banquet’ meals at Onsens which include Kobe/Wagyu beef, sea urchins and other expensive ingredients. Remember the soup (nearly always Miso) arrives last!
Part of a Kaiseki meal with decorated Quail's egg!

A few other things to mention:

There are always a host of restaurants offering most of the cuisine described above located in railway station concourses. Despite appearances they are generally quite acceptable.

Izakaya are a sort of pub/bar/cafe although their primary purpose is to sell alcohol. If you are struggling to find somewhere to eat they are a reasonable fall back option.

When travelling the Japanese like to snack and you are never far away from a convenience store (konbini) or kiosk selling Bento boxes. A Bento box is a wooden (posh) or cardboard (cheap) box separated into a lot of small compartments each filled with a different sort of sweetmeat. No long distance train journey is complete without one of these meals which are called EkiBen (Station Bento) and you can often find kiosks selling them on platforms.  
Picking up a Bento box on a station platform

A few words about convenience stores - konbini in Japanese. They are really everywhere and there are independents and local chains but it is the three main brands of Family Mart, Lawson station and 7 Eleven that proliferate. I once stood at an intersection and could see five Family Marts. Although predominantly food and drink they seem to sell everything, despite their size - newspapers, SD cards, USB cables, batteries, household and personal items etc. They also have ATMs and toilets - good to know in an emergency.

Convenience store food fare includes sandwiches (usually excellent with interesting flavours – particularly the egg ones), rice wrapped in seaweed and stuffed with meat or vegetable (futomaki sushi), steamed rice buns usually filled with pork and hot yakitori. The chocolate eclairs are also really good. Convenience stores are a cheaper alternative to Ekiben (Bento boxes sold on stations) when travelling by train.
One of 17,500 Family Marts in Japan!

Drinks vending machines are everywhere. They can be found almost anywhere – city streets, public buildings, parks, monuments and even on hiking trails. They sell a variety of hot (try the Royal Tea) and cold drinks (a wide variety of cold teas here) so there really is no need to carry fluids with you.
Plenty of choice - these drinks vending machines are everywhere

Street food: Unlike the rest of Asia street food isn't quite as universal but where it exists it is good (e.g. Dotonbori in Osaka). You can usually find a few stalls, selling Yakitori, Noodles or Okonomiyaki, near popular destinations or at local festivals. Snacks and sweets are also quite common.
Toffee apples

Drink - Tea, whether hot or cold, black, white, green, lotus (the list goes on) is the national drink. But the Japanese also have a bit of an obsession with whisky and seem to get through a lot of it. Beer is almost always a bland, lager style but Sake is just as popular. Served hot or cold Sake comes in a variety of forms from the very cheap to the eye wateringly expensive. It is worth a try.

And finally there are all the other unusual edible items to discover and even try!
Making Mochi - pounded glutinous rice
Eggs cooked in sulphurous thermal vents - lovely!

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