1. You don't need to tip
Speaking of restaurant etiquette, you don't need to tip in Japan. In fact, if you do, there's a big chance your server will run after you to give you the money you accidentally left behind. Waiters get paid a living wage in Japan, so don't feel guilty. This rule is also true for hotel staff and other service staff you'll encounter during your trip.
2. You'll need your passport if you want to do some tax-free shopping
Most mall stores offer tax-exempt shopping for tourists, but you need to have your passport with you to take advantage of it. Consider keeping a copy of your passport locked in your hotel's safe and keeping your passport on your person. You never know when you might stop to do some shopping.
3. You can't find an English explanation in a menu
Speaking of eating out, be prepared to encounter menus and signs with no English translations. If you are in tourist-heavy spots, especially in Tokyo, this won't be a problem. However, once you venture outside of the major tourist hot spots, it's common to see solely Japanese. This is where your list of Japanese words will come in handy, especially in restaurants. While many places will attempt to rectify this with pictures, it's still hard to tell what a miso-katsu is. If you don't have a list and there are no pictures, you can always pick a place with plastic versions of the menu items displayed in the window, and at the very least, point to what you want.
4. You are not allowed to point at people
Pointing at people or things with your finger, greeting strangers on the street with a friendly "hello," eating or drinking in public, and snapping photos of people without their permission are all big no-nos in Japan. It's also impolite to raise your voice or lose your temper in Japan, so be careful of how you handle situations that don't turn out the way you planned.
5. There are very few public trash cans in Japan
Actually, there are not much public trash cans put in Japan, even though it is known as one of the cleanest countries. Japanese people seemed to hold onto their trash until they were able to dump it at home, at a subway station, or at a coffee shop.
6. The metro is not 24/7
It may seem shocking that a country filled with so many conveniences doesn't have a 24-hour train system, but it's true, even in the glittering, well-oiled Tokyo. When planning your night out, expect to make a mad dash for the last train. Depending on where you are, you'll have to be through the doors anywhere between 11:30 pm. to 1:00 am.
7. Taxi is considered as the most expensive transportation
The public transportation in Japan, especially Tokyo, is very efficient and broad. For this reason, very few people take taxis during the daytime. However, the subways stop running at midnight so if you need to take a taxi during your trip, be prepared for the cost, which is higher than the cost in other countries.