Forget the Park Hyatt or the Imperial Hotel. If you want to enjoy the best of Tokyo but only need a nice bed and no luxury, there is still a chance you can find one.
However you will need to observe the following: Avoid the peak season (April, "Golden Week" in early May, October), and avoid weekends (Friday, Saturday night).
With the recent increase in tourists from the North Asia region (mainland China, also Taiwan and Korea), Tokyo is experiencing a shortage in hotel rooms. When in peak demand, the rooms that usually charge only 5,000 yen a night can go up to 20,000.
Areas to look for:
Try searching hotels in the Kita-Senju station or Minami-Senju station area. They are in the northeastern corner of Tokyo and it's an area for the working class so not many tourist sites around, but still well connected to central Tokyo by the JR and Metro line. In fact, the Metro Hibiya Line will get you directly to Tsukiji, Ginza and Roppongi within 20 minutes.
Some of the less-priced hotels in this area might come without a private toilet and bath. It's possible to find something for 5,000 yen or even less if the timing is right.
If you are travelling with a JR Pass and you don't have a late arrival/early departure out of Narita Airport, I suppose Shin Yokohama Station is also a possibility. Just use your JR pass to hop on the Shinkansen and you'll be at Tokyo station in about 20 minutes. Of course, if you are continuing on to Kyoto or Osaka, this would be a conveninent base too. A short ride on the local lines will take you to the center of Yokohama which is a beautiful port town plus they have the biggest Chinatown in Japan, so the dining options are plentiful. It's near the Nissan Stadium where the local pro soccer team, the Marinos, play their home games so you could add that to the itinerary.
It's completely out of central Tokyo, so a feasible option if you have unlimited rides on the Shinkansen or otherwise you will be spending too much to get to Tokyo.
Chains to look for:
The APA Hotel chain has been expanding at a rapid rate in Tokyo. They are known for very small rooms, but all come with a private bath, all the necessary items for a night stay. Breakfast might be included or offered at a discounted rate. They are usually within a five-minute walk from the nearest station making it ideal for using the public transportation.
One thing you need to look out for though, is that they tend to mark up their prices drastically when demand is higher. A room that normally sells in the 5,000 yen range could go as high as 20,000 yen on a weekend in April. Unless there are no other options, it's not worth paying that much for a room so small, so try looking for something else if you encounter such a high rate.
Toyoko-Inn is another player in the economic range and is the choice for Japanese business man on a roadtrip. Again, the rooms are very small and basic but usually come with free breakfast and some of the places even offer free curry rice on the evenings! Their prices can also change depending on the demand, but at least not as much as APA.
*And finally...those Capsule Hotels!
You might have heard about those sleeping pods, locally called "capsule hotels". There is a space just big enough for one adult to sleep in, and usually comes with a flat TV attached to one of the walls (see the photo above.) If you have a neighbor who snoors, you'll hear him all night long.
They are near at most major stations like Shinjuku, where the business man who has had too many drinks and missed the last train home might use them. There is a luxury version of it in Tsukiji ("First Cabin Tsukiji") which might actually be a good choice if you know for sure that you want to see the early morning tuna auctions.
While they generally come with a very large public bath area and sauna, they usually charge around 3,000 yen to 4,000 yen, so it's actually alot for a small pod with minimum comfort and privacy. But if you want to take home some interesting stories, perhaps it's worth a try.
Note that many capsule hotels only allow men to enter, though a limited number of them have women-only floors.
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