As a tourist in Japan you will face two main problems about food: “price” and “timing”.
You have a lot of souvenirs to buy, a lot of temples to see, and maybe you don’t want to spend a lot of money eating in Japan. But also, you don’t have much time to search for good restaurants, most of the time they are closed when you arrive late at night, exhausted by your journey, and you end up entering to the first convenience store you find to buy some prepared food…
You can do better than that.
The “combini” is one of the things you will love about Japan. A 24h nonstop store where you can buy from a hot drink to a good deodorant. Lawson, 7eleven, FamilyMart…you will soon get familiarized with them and maybe have a favorite. 
But let me tell you than the prizes in “combinis” are quite expensive comparing with a usual supermarkets. A bottle of tea or a piece of fruit can cost twice the prize…so I only recommend it when supermarkets are closed and you are in a hurry. 
If you want to find some offers, you have to come at the end of the day. Then they put offers to certain products (“onigiris” and other thinks they cannot sell the next day) the prizes become really cheap…but you have to risk yourself not finding what you were looking for.
"Combini" delicatessen
"Combini" delicatessen II
If you plan to eat during a “shinkansen” journey or in your hotel, it’s really interesting for your budget to stop by a supermarket. There’s a lot of them and if you have any doubts you can ask to your accommodation staff where is the closest one. 
In a supermarket you will find everything you could need, and really cheap. From fruit, drinks to prepared “bento” with all kind of freshly prepared food.  Maybe the boxes are not as fancy as “ekiben” but a lot cheaper. 
For me, the best option if you are late for the regular restaurants, want a quick service and freshly made food.  Also is really useful if you don’t speak Japanese and don´t want to have to talk with locals. You only have to buy a “meal ticket” at the entrance from a vending machine, then go inside and give the ticket to the staff. In less than two minutes you will be enjoying your meal. These kind of restaurants mostly serve donburi, ramen, curry and other simple but delicious Japanese traditional meals. You will have free water or tea so you don’t have to pay for the drinks, so they are a cheap way to eat in a restaurant.
Ticket meal near Kyoto Station
In our favourite Tokyo's ticket restaurant
Another meal from our favourite Tokyo's ticket restaurant
Best ramen ever, in Akihabara ticket restaurant

Merche Moreno