Guide To Using Japan’s Train Transportation System

The train system is the most common and efficient way to travel through Japan. If you’re going to travel there for the first time, you’re going to probably plan your routes around the trains. However, when you get there, you might become intimidated and confused like I was. 

That’s why I decided to write up this guide so you don’t have to struggle like I did! I’m a believer I was led to experience some mishappenings as learning experiences. Even though, according to Reddit and from some Japanese locals, some people still struggle with the train system until this day.

Even with this guide, it may not lead you completely free of confusion, but it is always better to be prepared to learn before you attempt to figure it out yourself and save yourself the anxiety of thinking you’re going in the wrong direction or doing it wrong.

I also have to note, it is best to absolutely try to not use taxis or rideshare apps as much as possible for going to some locations because they are most costly than taking trains. I do think taxis can be useful in some instances when you really need to (for example, too tired to walk) or want to avoid long waits to your stop. However, timing is absolute key to getting in time to your destinations when using trains.

Whether you have some experience with trains or live in a metropolitan city, each train (or subway) system in each country will run a little different. You might not even have any experience with trains so I want to break down parts.

Things to know first

The trains in Japan are not operated by just one company but ran under several companies. It started with The Japanese National Railways (JNR) once in charge of all the trains but eventually split into six different companies that now all fall under the branch of Japan Railways Group (aka JR). With that being said, this will explain when you look at the ticket buying machines, you might find some of the same routes or directions with different prices and that is based off the companies’ set of prices. With those that are not part of the Japan Railways Group, they can be private companies.

There are a few different types of trains that will help you determine which train you need to get on:

  • Local trains – These trains are best for shorter distance routes and not recommended for longer ones. These usually connect to one stop to another (or think of it as Point A to B). 
  • Express trains – These trains are best to help you transport to airports like Narita International Airport and Haneda International Airport, but these trains aren’t as common anymore with the use of Limited Express or Rapid ones.
  • Limited Express trains – Limited Express trains are the ones that go to the major or popular stations. They’re the fastest trains aside from the bullet trains. A popular train that is an example of this is Skyliner, which also connects well to Narita International Airport (NRT).
  • Rapid trains – This can go shorter distances too like the Local trains, but what differentiates them from Local ones is that they can skip over other stops than go uniform from Point A to B.
  • Shinkansen (or the bullet trains) – You’ve probably heard about these being one of the fastest types of trains in the world and they are really, really fast and an amazing experience. They can go as fast as 200 mph and can take you to regions distant from each other in a shorter amount of time vs. if you drove.
  • Special trains – These trains were designed for aesthetic purposes but also transportation purposes. They usually go through more scenic routes and were designed to have a pretty, stylish but cozy experience.Most, if not all, of these trains would be considered for luxury, sleepers, cuisine, and/or sightseeing.

When looking out for tickets, you might also notice there’s the Tokyo Metro and the Toei Subway. These are both two different subway systems that connect to areas of Tokyo and because they are, tickets will not be transferrable and must be purchased separately. The JR Pass will not be worth it if you’re traveling to these subways because JR Passes are fit for Shinkansen or Limited Express trains. There may be some routes where you have to criss cross to a JR line in Tokyo subways (for example, the JR Yamanote Line or JR Chou Line).

Japan bullet train called Shinkansen
Inside the bullet train or Shinkansen
Shinkansen views in Japan
These are some of the most beautiful views you’ll get when you ride the Shinkansen
Skyliner train in Japan
The Skyliner train

Apps to use or rely on

Having an app on hand will be the most useful thing when going through Japan’s trains. I used Google Maps thoroughly on my trip and find it super useful! It tells you in details and changes up in real-time what route to follow along, what trains to catch, as well as the shortest time to get there. With your route too, a price will be included at the end to tell you how much the trip would cost you through tickets.

Another decent app is Rome2Rio where it can tell you too how long, how much the tickets will cost, what trains to catch, and the route, very similar to Google Maps. But I prefer Google Maps because its design is easier to follow along.

All you have to do with these apps is input the location you want to go. Make sure the train mode is on display.

Toei Subway

Understand the components of a train ride

So you’re using one of the apps I mentioned above, but you kind of don’t know how to read it right? I will break down what each train ride’s route consist of and to pay attention to.

  • The station
  • The line (it’ll have a letter to represent it) – This is where you will have to follow along the route if this is a JR Line.
  • The platform (also called as “track” with a number to represent it) – These will tell you whether you should stand on the left or right and wait for the train on that side.
  • The car train – There will be numbers posted on the ground or against a guardrail and this isn’t always the most important piece to go by, but it is recommended to get into the car train your Google Maps tells you so you can get out closer to your exit. There may be a queue line, so you want to stand behind the people standing on there first.
  • The stops to pass through
  • The exit – When you’ve reached to your final station/stop, you need to follow signs that will tell you which exit to head towards.
  • Your seat number – This is only if it’s reserved on a Special train, Limited Express, or Shinkansen. It’ll be on your ticket.

See this chart for what to look out for:

This is from Google Maps

Here are other things to keep in mind:

  • Understand how many stops you have to make when you get on a line/station.
  • Make sure to see if there is a mention to transfer lines/stations.
  • There is a “walking maps” option on Google Maps that can tell you where to walk to find your next station if you’re transferring.

Pin this for later!


Before you buy tickets, maybe consider an IC card.

This is something I wish I had gotten before my whole trip became going to the ticket machine after another! IC cards are basically pre-paid transportation cards that can be recharged by having the ability to fill more money in it, that way you can easily scan these through the ticket gates. They save you time once you have enough funds in there and you don’t have to waste anymore time by waiting for ticket machine lines or printing tickets out (nor risking losing a ticket as easily). All you have to do with using these cards through the gates is tapping them on the digital scanners.

The two most popular transportation cards are Suica and Pasmo, which can be downloaded as apps too. Suica and Pasmo are useful rechargeable types of cards for a lot of the subways.

However, sometimes they do run out of selling these physical cards at many places, which is why I was no longer able to get them and I had one opportunity to at a popular station but forgot to get it. When you stumble upon this offer such as when you’re on a ticket counter line to buy a Skyliner ticket, ask for this offer right away or if they sell the physical cards.

When buying tickets, pay attention to the boards above the ticket machines.

There will be boards of maps located on the wall that will show the different routes to take. These boards are used for you to figure out how much you should pay going to that stop (there will be a 3-digit number above it), which is how much yen you will pay. 

For example, Yoyogi Station will say 220 yen on the board. Some map boards can be absolutely confusing when you look at it and you might spend a long time looking for what to look for, but luckily ticket machines have a “search” option where you can just type in the station name. This will be so much easier.

Map board in a Japan train station
Japan train ticket machine

Have your full attention on finding the right signs in a station.

When you end up in a wrong line, track, or platform, that will make or break your smooth train traveling experience. However, this is completely preventable if you pay full attention to where to walk to by looking at the signs and seeing if it matches with your route as shown on your Google Maps. This is an easy mistake to make when you first try to figure out the train transportation in Japan.

That is why the components I listed above are so important to look out for and to make sure the signs match up to that.

Keep track of your time.

Time is what trains go off of for an estimated arrival, and sometimes, there can be delays, but don’t fret when that happens because the apps can be on real time (especially if you opt for notifications and pin the route to your Google maps app), and you just got to wait. You could also see on your Google maps app too when a train is oncoming and that can be important if you’re trying to make it to somewhere on time, so definitely keep track when a train is estimated to come. Some trains only take a few minutes to come if you missed one already. 

One of the most important things about keeping track of time is when you’re in the train already. This is when it’s so important to pay attention to how many stops you have to wait to pass until it’s your time to get off. The app will highlight how many stops there are until it’s your final stop. Trains will have digital boards to show you where you are. There are AI voices announcing over the PA what the stop is and what’s next, and if you happened to miss those two things, there will be boards located on the walls of the station outside of the train that will tell you where you are and what stop is coming up next.

What happens if you missed your train or ended up on the wrong stop? This might seem nerve wracking, but rest assured, if you were in the right station to begin with, you have a chance to get back to where you’re supposed to. Most trains have another train parallel on a stop, but not always the case if this is not the same type of train like a Rapid Train for example. However, if it is the same type of train like a Local one, you can easily hop on the train parallel to the one you just got off and it can take you a stop or a few stops back (depending how many you missed) or the stop you were just on and just walk yourself to the right place of that station. If it isn’t the same type of train, you can refresh your Google Maps and find a route from where you are on how to get to your actual station.

Keep in mind that most trains close by midnight and then they stop until possibly around 5am again. You’ll actually have to confirm through on the last route that will be running as stated on the app. So, try to not be out too late somewhere as a tourist and get stuck unless you’re willing to pay for taxi to come and get you, which can sometimes be an affordable option depending on distance and lack of surges. GO is Japan’s known taxi rideshare app and they also use Uber, Grab, and DiDi there; most of these won’t be private drivers but part of taxi company services.

Don’t be afraid to ask for help at help centers or information desks (that’s what they’re there for).

This is probably the most helpful experience of my train transportation journey in Japan. These information desk workers are so helpful and many do know English (although if they don’t, make sure you have a translation app with you). Sometimes the map boards will show their routes in Japanese and not have an English version at all, so you can simply walk up to a desk and ask for how much a station will cost, as well as directions to go to a specific station or if you need further clarification on something. 

How to use the tickets or IC card through the gates

Every station will require you to get through the gates by the use of your ticket or IC card. It is important even if a friend or family member has an IC card with a lot of funds, you should have your own. Since there will be so many people at these train stations, let people who are ready to get through the gates go first until you have your card or ticket out to scan them through than blocking the way. Just move out of the way and stand back if you’re looking for it.

Sometimes you might lose track of how much funds is in your card, but you can simply recharge it by going to a ticket machine. Sometimes, when you scan your ticket through the gate that it will tell you if there isn’t enough and you must add more to it, so you can go to a help desk for someone to help you on that and you’ll just end up paying a little more to adjust the ticket. Some stations will also have fare adjustment machines, so make sure to keep your eyes peeled for the ticket machines.

Save yourself some stress by researching routes.

I did not have time to do this for my trip to Japan, but I think if you can dedicate some time to it, I guarantee this will save you some stress and confusion on where to go and get off at in trains. You can set up a note in your phone’s “Notes” app outlining the details ahead like you would see in Google Maps and studying that before you head off to the jungle. Concrete jungle, that is.

Inside a Japan subway

I hope this simplified guide helps you out in some ways! It’s the closest way I can explain the way Japan’s train transportation is to fit it as a generic guide for all types of trains and stations as all stations are built different. Good luck!

My last piece of advice: Take some time to explore some of the stations! These stations will be some of the coolest ones you’ll see in your life (especially Tokyo Station). There are a lot of convenience stores with delicious fresh foods and snacks, some shopping stores, some really good bakeries and Japanese fast food restaurants, some bookstores, and even some gacha areas. Gachas are the vending machine toys.

Japan train station
The train stations in Japan are some of the best stations with the best food and more!

Tell me what you thought below!