IMPORTANT: First! You will need a sim-lock free phone, phones are usually sim-lock free unless its bundled with a contract in your home country, some countries still allow the carriers to sim-lock the phone just to make sure the consumer will stay loyal to the phone carrier. Just make sure to double check.
Then, there are a couple ways which you can get your sim card for Japan.

1. Pre-order it online and have them ship the sim card to your hotel/ accommodation.
2. Get it at the airport! Shops in airport now offer data sim for short stay and they will also kindly setup the card for you!
3. Electronic stores, places like Bic Camera, Yodobashi Camera do have data sim in stock, just ask the staff for help and they will guide you through the process.
4. Besides actually retail shops, vending machines for data sim are also available in the airports like Narita, Haneda or Fukuoka.
Now, pick your sim card. There are now a LOT of tourist friendly sim cards out there comparing the 2 or 3 years ago since companies now realize how big the market for tourist sim is. And thanks to the competition, services that tourist sim cards provide come in various price, speed and volume.

Price varies depending on volume, speed as well as the usage duration. You can pick the one that you want depending on your situation and budget.
IMPORTANT (again): Make sure you pick the right size for your phone since most of these sim cards come in with Normal, Micro and Nano size.
When it comes to the most common sim card nowadays, it will be the IIjmio Japan Travel Sim.
It comes in with two packages, 1GB/30days or 2GB/3months, which I think is more than enough if you use it mainly for navigations and SNS. What great about it is that it also comes with a 050 phone number which you can make calls using the internet with a dedicated smartphone application!
If you are planning for a longer stay or is a heavy user, the So-Net data sim offers a 12GB sim that will last 6 months.
Help this guide can help you with the process of choosing sim card, here in Japan.
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