Confused about how to use trains in Japan? This first-timer’s guide breaks down everything from the JR Pass to local train tips, station navigation, and must-know etiquette—so you can travel Japan with confidence.
Confused about how to use trains in Japan? This first-timer’s guide on how to use trains in Japan breaks down everything from the JR Pass to local train tips, station navigation, and must-know etiquette-so you can travel Japan with confidence and enjoy delicious ramen.
The first time we set foot in a Japanese train station was right after landing at Narita Airport. Jet-lagged but buzzing with excitement, we had one mission: get to Tokyo.
Thankfully, we had booked the Keisei Skyliner Train a couple weeks in advance through Klook, so we already had a plan. As soon as we cleared customs, we made a beeline for the airport’s train information booth. The booth can be found in the basement near the baggage claim and the exit. The staff printed our tickets, pointed us in the right direction. Off we went— rucking with our bags past signs in Japanese and English, looking for the right track and platform.
After a few minutes of scanning the signs and checking our tickets again (and again), we found it. We stood there on the platform, watching trains arrive and depart with quiet precision, barely able to stand still. We were finally in Japan—and our adventure was officially beginning.
Japan’s train system can feel intimidating at first, but once you get the hang of it, it’s one of the easiest and most efficient ways to explore the country. In this blog, we’ll walk you through everything you need to know and how to use the trains in Japan. From navigating stations like pros to understanding train types, using IC cards and the JR Pass, and even avoiding common mistakes we made on our first trip.
If you’re planning your first visit to Japan and want to feel confident the moment you land, this guide’s for you. Let’s hop aboard
The Tokyo Metro Pass. Is it worth it?
Once we were getting settled in Tokyo, we quickly realized just how massive—and connected—the city’s train system really is. Trains and subways are the heartbeat of Tokyo. You’ll likely be riding them multiple times a day just getting from one neighbourhood to another (Trains are faster than passenger vehicles too!).
That’s where the Tokyo Metro Pass for train travel comes in—and it’s definitely worth it.
We purchased a 3-day (72 hour) train pass through Klook and picked it up at Ueno train Station after riding the Keisei Skyliner train in from Narita Airport. The process was smooth, and the pass came in handy immediately. Instead of buying individual tickets every time we hopped on a subway, we could just tap in and go with our phones and the Suica Apple Wallet feature no fumbling with cash, no figuring out the fare chart. Just swipe and ride.
If you’re planning to explore Tokyo in depth and by train—think hopping from Shibuya to Asakusa, then over to Ueno and back to Shinjuku—the Tokyo Metro 24-, 48-, or 72-hour pass might save you money and time. The pass gives you unlimited rides on both the Tokyo Metro and Toei Subway lines (note: it doesn’t include JR lines like the Yamanote Line, but more on that later).
A few quick things to know:
- -You can buy the Tokyo Metro Pass at Narita or Haneda airport, or online in advance (we used Klook).
- -The countdown starts from the first time you use it, not when you buy it—so plan accordingly.
- -It only works on Tokyo Metro and Toei lines, which cover a huge chunk of the city, but you’ll still want to check if your destinations are on a JR line or not.
How stations are numbered:
The alphabet letter represents the subway line name.
In the subway route map, the station number is shown according to subway line.
Station numbers are circled with a color that represents the subway line.
It’s perfect if you’re spending a few days exploring Tokyo before heading to other parts of Japan. And even if you’re using a JR Pass for intercity travel, we found it was still worth getting a Metro Pass just for getting around Tokyo itself.
Next, let’s break down the different types of trains and lines you’ll see in Japan—including how to spot the difference between local, rapid, and express trains (yes, it matters!).
JR Line
In Tokyo, many visitors use the Tokyo Metro or Toei Subway passes to get around—but it’s important to know that not all of Tokyo runs on the subway system. Some major areas and attractions are actually best accessed using JR trains, especially the JR Yamanote Line, which loops around key neighborhoods like Shibuya, Shinjuku, Harajuku, Ueno, and Tokyo Station. So even if you have a metro pass, you’ll likely still need to use JR trains at some point—especially for day trips or airport transfers. If you’re using an IC card like Suica or Pasmo, it works seamlessly across both systems, making it easy to tap between metro and JR without worrying about separate tickets.
If you’re traveling around Japan, and not just in Tokyo chances are you’ll be using the JR (Japan Railways) Lines—a massive network that covers everything from city subways to cross-country bullet trains. Whether you’re planning to explore Tokyo, hop between major cities, or just get to the airport smoothly, knowing how to use the JR system will make your trip a lot easier.
What are JR Lines?
The JR Group is made up of several regional rail companies that used to be part of the government-owned Japanese National Railways. Together, they cover most of the country, including:
- JR East (Tokyo and the Kanto region)
- JR West (Osaka, Kyoto, Hiroshima)
- JR Central (Nagoya and the Tokaido Shinkansen)
- JR Hokkaido, JR Kyushu, and JR Shikoku for their respective regions
Within cities like Tokyo and Osaka, JR runs local trains (like the Yamanote Line), while for long-distance travel, JR offers the famous Shinkansen (bullet train).
Why use JR Lines?
They’re convenient – Many major city hubs, tourist attractions, and airports are directly served by JR.
They run on time – Trains are famously punctual, with delays rare and usually just a few minutes if they happen at all. On our JR train from Kii-Katsuura to Osaka, it was delayed due to a fallen tree. It was delayed for hours that we had to bus another line and use that train back to Osaka.
Tips and Tricks for Riding JR Trains
1. Get a Japan Rail Pass (if it makes sense)
If you’re traveling between cities (like Tokyo → Kyoto → Osaka), the JR Train Pass is a great deal. HOWEVER, it is not worth it if you are staying at each city for a couple days since the JR Train Pass has gotten a lot more expensive over the years. We travelled from Tokyo, Kyoto, Tanabe, Kii-Katsuura, and back to Tokyo for our two week vacation and did not get the JR Pass.
2. Use IC cards for local JR trips
Suica or Pasmo (in Tokyo) and ICOCA (in Kansai) work on most JR lines and subway systems. Just tap in and out—no need to buy individual tickets. This was so nice and convenient to have.
3. Look for green signs
JR stations and signage use green branding. Look for the green JR symbol when navigating busy stations. Google Maps is also such a good resource and will be your best friend for your travels around Japan.
4. Check the train type
Just because it’s a JR train doesn’t mean it stops at every station. Make sure you’re not accidentally boarding a rapid or limited express train if you need to get off at a local stop. This happened to us a couple of times. Some trains are express trains and will skip stations, be sure you are looking at the right train and the right departure time.
5. Download helpful apps
Use Japan Travel by Navitime or Google Maps to check train times, platform numbers, and fares in real time. They’ll also tell you if a JR Pass covers your trip. Like we stated above, Google Maps is your best friend.
6. Reserve seats for longer rides
For the Shinkansen and limited express trains, you can reserve seats at a JR ticket office (look for the “Midori no Madoguchi” window) or ticket machine. JR Pass holders can reserve for free. For a small fee, you can typically reserve a seat for your train ride, and sometimes it is so worth it, instead of standing the entire train ride.
Train Classes and Seat Reservations in Japan
When traveling long distances by train in Japan, you’ll typically have a choice between Ordinary and Green Car (business class) seating. On select Shinkansen routes, you’ll also find Gran Class, which offers a first-class experience with even more space and luxury. Most local trains only have ordinary seating.
Green Cars are quieter, roomier, and often less crowded—perfect if you want a bit more comfort—but they usually cost 30–50% more than regular seats. Gran Class takes it a step further, with reclining seats, complimentary drinks, and an ultra-relaxed atmosphere (at a premium price).
Shinkansen and limited express trains usually offer both reserved seats (shitei-seki) and non-reserved seats (jiyū-seki). Some trains, especially during peak seasons, operate with only reserved seating. Green Cars are often fully reserved, meaning you’ll need a seat reservation to ride in one.
On most local, rapid, and express trains, all seating is non-reserved—just hop on and find a spot. If you’re using a Japan Rail Pass, seat reservations are free and can be made at ticket counters or machines. Otherwise, expect to pay a small fee, usually between 300 and 900 yen.
Purchasing Tickets
One of the easiest ways to get around Japan is by using a prepaid IC card like Suica, Pasmo, or Icoca. These cards let you tap in and out without worrying about ticket prices or language barriers.
If you’re not using an IC card, don’t worry—buying individual tickets is still simple. For shorter trips, you can use the ticket machines found in every station. For longer distances or when you need to book a specific seat (like on the Shinkansen), you’ll want to go to a staffed ticket counter or use a more advanced machine that handles seat reservations.
a) How to Buy a Ticket from a Machine (Short-Distance Travel)
Look up the fare
Above the ticket machines, you’ll see a large map showing nearby train lines and stations. Find your destination and check the fare listed next to it.
Insert your money
Machines accept most Japanese coins (10, 50, 100, and 500 yen) and 1000 yen bills. Some machines also take larger bills or allow IC card payments.
Select how many tickets you need
The default is one ticket, so if you’re traveling solo, you’re good to go. If you’re with friends or family, choose the number you need.
Pick your fare amount
Tap the button that matches the price for your destination—for example, 200 yen.
Grab your ticket and any change
Your ticket and change will come out below. Make sure to collect both before heading to the gate.
b) Buying a Ticket at the Counter
If you’d rather speak to a person or need help with seat reservations, you can buy your ticket at a staffed JR ticket counter (often called Midori no Madoguchi). To make the process quick and smooth, you’ll need to give the following details:
- -How many people are traveling
- -Your travel date
- -Departure and destination stations
- -Whether you want an ordinary seat or a Green Car (business class)
- -If you prefer a reserved seat or are fine with non-reserved
If you’re reserving a seat, it helps to also know:
- -The train name and number, or
- -The exact time you’d like to depart
If you don’t speak Japanese or feel unsure, it’s a good idea to write down all this information and hand it to the staff. Some stations even have special forms—sometimes in English—that you can fill out ahead of time. They’re not used often, but they can be really helpful during busy periods or when there’s a line.
Special Trains
For travelers seeking a unique and fun sight seeing train journey through there Kansai region, the Aoniyoshi sightseeing limited express offers an exceptional experience for a really affordable price. We took this train from Osaka Namba station all thew way down to Nara to go see some deer. It was a really cool and fun experience. The train connects Kyoto, Osaka and Nara.
Spacious Seating
Twin Seats: Arranged in a 1+1 configuration, these seats face eachother with a wqooden table in the middle, ideal for couples or travelling pairs.
Salon Seats: Designed for groups of 3-4, these semi-proivate compartments offer a cozier setting with a large table.
Onboard Amenities
Passengers that are riding this train can enjoy a mini library in Car no. 4, featuring books related to the region along the route. Additionally, in car no. 2 you can expect to find local Nara specialities including exclusive desserts, coffee, and sake.
Tips and Tricks
To board the Aoniyoshi, passengers need:
1: Basic Fare: Covers the standard fare between stations. This is something we did not realize when booking this train and some other trains. Even though you are booking a seat on a train, you need to also purchase the basic fare to get onto the train.
2: Limited Express Ticket: This is required for all limited express trains on the Kintetsu line.
3: Special Car Ticket: An additional fee specific to the Aoniyoshi.
TICKETS OPEN UP 30 DAYS BEFORE DEPARTURE. BOOK AS SOON AS YOU CAN!!!!! THEY SELL OUT FAST
Train Etiquette
Always let passengers get off the train before you step on. It’s a small gesture, but it’s part of the everyday courtesy you’ll notice across Japan. At busy stations, try not to stand in the doorway—especially during rush hour when trains can get packed.
If you’re carrying a backpack, either place it on the overhead shelf or set it on the floor near your feet to avoid taking up extra space or bumping into others.
Inside the train, things are usually quiet. Most people spend their time reading, scrolling on their phones, or even napping. While it’s fine to use your phone silently, talking on it is generally not allowed—unless you’re in the designated areas near the doors on Shinkansen or limited express trains.
Train announcements are typically made in Japanese, but on Shinkansen and routes popular with international travelers, you’ll also hear them in English. Many newer trains have screens that show the next station and transfer options, making it easier to stay on track—even if you don’t speak the language.
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