The trains in Japan is a phenomenon that has tourists flocking to use them. Yes, it is cheaper using the trains and buses to travel around. However, there are a few things people outside of Japan need to understand about taking the trains. Once you understand the culture of the trains then you can see why the tales of its efficiency has reached international fame.
In Japan, there are a few types of train lines available and it is good to know the different rails available. The major and most common one you will see are the Japan Rail lines or JR for short. As convenient as the JR lines are, there are some popular places located far away from the JR stations. To compensate there are subways, metro, and private rails available. Be sure to pay attention to the signs on the train to make sure you are boarding the right train as some share the same platform.
Before boarding the train, see if it is a local (普通), local rapid/ semi-express (準急), rapid (快速), express (急行), or limited express type (特急). Depending on the designation will determine how many and which stations it will stop at. The local makes a stop at every station, but the semi-express does not. The difference between each one is not only the amount of stops they make, but the frequency they appear on the line too.
When purchasing a train ticket first you need to figure out the line you will be using. For example, are you going to use the JR line or Metro. Both have separate machines where you can purchase their line specific tickets. These, ticket dispensing machines, can usually be found near the ticket turnstiles. Once you figure out which train you will be taking then you need to figure out the amount you will pay. Unfortunately, the machines do not have the name of the station to choose from, but instead there are various prices. There is a large map above the ticket dispensers with the names of the station with a price under it. Once you find your destination choose the amount to be paid and insert your money. Your ticket will be dispensed below so do not forget to take it with you.
For more advance travelers, there are special single to multiple day passes people can purchase at the machines or Midori no Madoguchi ticket office. These tickets are a nice alternative if you plan taking multiple trains within an area. For example, the Tokyo Metro passes cost 600 yen for a 24-hour period and works on all Tokyo Metro lines. If your targeted destinations can be reached on the metro lines and your traveling exceeds the 600 yen then the pass is worth it.
If you had just finished purchasing your ticket, head towards the turnstile. There are two types of turnstiles, one is for IC cards like Pasmo and Suica, and the other is for tickets. You can identify them by the color. If you see green or pink then only IC cards can be used to go through. The black ones accept tickets and IC cards. When inserting a ticket do not forget to retrieve it from the next slot. Otherwise you will have to pay for it again at the help counter. Upon exiting at your destination turnstile, the ticket will not come out again after you insert it.
Waiting for the train requires you to line up in an orderly fashion. Sometimes you will see queue lines painted on the ground to help you figure out where to line up. Other times there will just be a marker to indicate where the doors of the train will be. At this time people create at least two lines because once the train comes they stand to the right or left of the doors and leave the center open. They do this in order to let the people who are getting off the train through. Do not rush the door or cut the person in front of you. As long as you follow the flow you will be in the train in no time.
In the morning, Monday to Friday, at around 7am to 9am the trains are pretty packed depending on where you are traveling from. This is especially true in Tokyo, so if you plan anything, watch out for these times. If you plan it properly you will not end up being pushed into the trains with people invading your personal bubble. If you want to experience the morning rush go to one of the busiest stations, like Shinjuku, close to 8 am and get on the Chuo-Sobu line.
If you have never ridden the train in Japan, you will notice that most of the time it is quiet. There is an unspoken rule to not talk on the trains, but it is not explicitly followed. Certain situations invoke specific conducts. For example, if you see someone sleeping on the train then do not have a loud conversation with your friend near them. Also, do not talk on your phone. If you have to answer the phone please go to the area where the train cars connect. You can close both the doors and the sound will be muffled from everyone else.
The seats in the train have a priority aspect to them. If you see a handicapped, elderly, or pregnant person offer them your seat. Eating and drinking on the regular trains is somewhat a taboo. If you plan on listening to music while on the train then make sure it is not too loud that the person near you can hear it.
At first all of these rules, spoken and unspoken, seem to be daunting to many foreigners, but as long as you respect it you will have a pleasant time on the trains. See how everyone acts and use it as an example to how you should conduct yourself. After riding the train a few times, you will start doing all of these things out of habit.