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1.   Airport to Tokyo
-      From Narita: You have multiple options. You can opt for the fastest and easiest way which is the Narita express. For about 3,000 yen and a 1 hour ride, the Narita express will take you straight to the center of Tokyo. You can also choose the bus, about 2,500 yen and a 1.5hour ride. For those who already know their way, for 1,500 yen you can join Tokyo’s center using the Skyline express in about 2 small hours.
*Recently, you can find a bus departing from Narita terminal 2 that will take you to Tokyo station for only 1,000 yen.

For more information https://tokyocheapo.com/travel/transport/cheapest-transport-to-and-from-...
-      From Haneda: Join Shinagawa using the Keikyu line. From Shinagawa you can directly ride the Yamanote line to Shinjuku station. The trip takes about 45 minutes and costs about 600 yen.
For more information 

2.   Train in Tokyo
-      Once in Tokyo, you will mainly travel using the train. The lines are mainly divided between the JR lines and the Tokyo metro lines. The price of a trip is determined by the distance travelled. Note that you may need to transit form a train/ line to another. In the event you transit from a JR line to a Tokyo metro line, you will need to buy another, new ticket. To avoid this fastidious step at each connection, we recommend you to get a Suica or Pasmo card.
-      Suica/Pasmo cards: These cards are like virtual digital wallets. You can acquire the Suica card it any JR station counter, and the Pasmo card at any Tokyo metro station counter. They both cost 500 yen, refundable if you return the card. The concept is simple, you charge your card with money at any station vending machine and you just swipe it again the card reader at the train platform's entrance. The fee for your journey will be automatically deducted from the card as you swipe it at the station's exit! You can also use these cards to pay numerous services, such as convenience stores, taxis etc.
-      Teiki-ken (Periodic commute pass): You can equip your Suica/Pasmo card with a commute pass. In order to do this, use the vending machine, and follow the instructions. You get a great discount on a distance travelled on a daily basis by buying a commute pass instead of buying tickets.
3.   Bus in Tokyo
        There is an uncountable number of bus lines in Tokyo. It surely is trickier to understand at first, but finding the right bus for your commuting needs may just be the best option for you!
There are two types of buses:
-      The one with a flat rate: You pay the announced fare at the bus door, regardless where you are going to get off.
-      The travelled distance rate. You get a ticket as your get on, and pay for the travelled distance at the same machine, before getting off.
4.   Taxis in Tokyo
 Taxis in Tokyo are literally everywhere. The base fare is quite reasonable at 410 yen for the first kilometer. However, it climbs up at a rather fast pace. Count about 5,000 yen for a 20-30 minutes ride and don’t forget that traffic in Tokyo can be pretty heavy. Although it can be a life savior sometimes, it definitely remains an expensive means of transportation in Tokyo.
5.   Driving in Tokyo
The following information’s accuracy depends on the country your driving license has been issued from. Please refer to the JAF website for eligibility information.
-      Staying in Japan for less than one year: You are allowed to drive in Japan with an international driving license or a Japanese translation of your driving license. You can have your license translated at the JAF office (about 3,000 yen).
-      Staying more than a year: If you’ve been in Japan for more than a full year, you now need a Japanese driving license. You can acquire one by simply applying for it at the driving license center in Shinagawa. You will need to have your original license translated at the JAF office first. Depending on your origin country, you may be required to pass a written and/or driving test.
Although the roads are safe and the driving experience in Japan relatively easy; driving isn’t the best option if you reside inside Tokyo. It is pretty expensive and not the quickest way to travel. Driving will be reserved for weekend excursions etc. 
6.   Bicycle in Tokyo
-      It may be the best way for you if you to travel, especially if your workplace/school isn’t too far from your living place. In some cases, on top of being free, it is also by far the fastest way to get where you need to go. Japan being perfectly safe, you don’t have to worry about having your bicycle stolen or damaged. Note that despite our best effort, we cannot always guarantee bicycle parking spaces at our properties.

Settle in, first steps

7.   Residence card
This is the first thing you want to do when arriving here. You will need it for absolutely everything.
In some cases you may just get it straight at the airport as you arrive. In other cases you will need to go to the ward office of your living area to get it. In all cases, you will need to provide a proof of residency featuring your address, and register it within 14 days.
For more information please inquire to the ward office of your living area.
8.   Opening a bank account
You will find that you will need it for a lot of necessary tasks, such as getting a phone or subscribing to some services etc.
Depending on your visa status and your employment situation,  the range of bank that will accept to open an account for you may vary. However, you should be able to open one at the Japan postal bank or Shinsei bank, on presentation of your resident card.
9.   Get a phone
           Subscribing to a phone contract can be difficult for foreigners, but here are some options:
-      Classic Japanese carriers: NTT, Softbank and AU. Typically these are 2 years contracts (cancellation fee about 10,000 yen). You will need your resident card and a bank account at the minimum. For about 9,000 yen a month you will get a brand new phone, a phone line, and a data package. This is the most functional way there is.
-      Data sim cards: You can also opt for a sim card only. Their flexibility and price won them their relative popularity. Available in most electronic stores, you can choose a phone number, the amount of data per month you want, or just choose to pay just what you used. Note that the quality is significantly lower, and you will need an unlocked compatible phone to use one of these.
10.               Health insurance
If you stay in Japan exceed 3 months, you are required to register to the health insurance system. The procedure is done at the ward office of your living area. Note that this is not optional, and if you stay in Japan, sooner or later you will be required to pay the fare for the totality of your stay from its beginning. The health insurance covers 70% of your medical fees. Please, inquire to your area ward office for more details.
11.               Withdrawing money
-      It may depend on the type of card you have, but your credit card will probaly be denied in most ATM. Some of the ones you should be able to use are the 7/11’s ATM and the Shinsei bank’s ATM.
-      You can find money exchangers in every big train station and in most shopping districts.
-      You can also have money transferred from overseas, but in most cases the fee are expensive and the procedure is fastidious.

Daily living

12.               Bills (Utilities, phone etc)
Although a good deal of people opt for auto credit card payments, for foreigners it can be a little less easy. If you don’t have a Japanese credit card, or simply wish to be sent payment forms, you can choose this option. In that case, you will receive bills in your post box. Usually, prior to the actual bill you will receive a notification to let you know how much your soon to come bill will be. The actual bill features a bar code, take this one to any convenience store to pay it off in cash.
         *If you fail to pay your utilities on time, the service will be cut off. In that case, you will need to contact the concerned company after settling your balance, to have your service re-activated.
13.               Shopping in Tokyo
-      Groceries: You will find numerous grocery stores in Tokyo. From the convenience stores to bigger supermarkets, and even Cost’co! The prices vary from a brand to another, so don’t hesitate to explore and compare.
-      Housing/Furniture: You can easily find home centers such as Shimachu, Nitori and even Ikea here. All our properties come furnished, but for those who would like to add a personal feel to their place, there are enough options! Most of these stores offer delivery services as well.
-      Medicine/house maintenance: While you can find these in some supermarkets, the place to go is the drug store. You find them everywhere just as convenience stores.
14.               Garbage disposal in Japan
After the dramatic pollution problems Japan suffered from post-war, we can now say that the country is big on garbage disposal regulations and recycling. Garbage must be separated and disposed of, according to a garbage collection schedule that will vary depending on the area.
Everybody here follows these rules, and not doing it will not be accepted by your neighborhood. Depending on where you are from, it may be a completely new thing to you, but consider it as one of the most important too.
*For garbage of large size or appliances, you need to contact the collection center of your living area and buy collection stickers at the convenience store, before getting rid of the items.
15.               How to fit in your new neighborhood
Although times change and Japan is a step at a time more open to foreigners residing here, keep in mind that only a very few percentage of the national population is from the overseas. Another variant, a comparatively very high percentage of the population is elderly. Put these together and you get a realistically still fragile Japanese-foreigner relation.
Avoid at all cost the followings to ensure the best integration possible into your new neighborhood: street smoking, littering, noise disturbance, bringing groups to your place in a very obvious manner, illegal bicycle parking, and irregular garbage disposal.
16.               Smoking in Japan
Although a lot of restaurants and other indoor places still allow smoking or offer smoking areas, note that street smoking is prohibited. You must smoke within the designated smoking areas.

Other tips

17.               Emergencies in Japan
Here are the emergency numbers in Japan:
-      119 for fire and ambulances.
-      110 for police.
The other possible emergency in Japan, earthquakes.
Please refer to the ward office of your living area for details about the earthquake refuges.
Here is a list of some of the indispensable items you want to have on the side in case of massive earthquake:
-      Flash light / batteries
-      Non-perishable food
-      Water
18.               Safety in Japan
Japan boasts incredibly low criminality records, and for a reason: it is incredibly safe. You can walk in any area at any time without risk. Same goes for your apartment, the likelihood of getting robbed in Japan is practically non-existent. Police are never really far away and aggressive individuals are really rare to come by.
Safety in Japan should not be of your worries. This being said, a little caution never harms.