How to Navigate Japan’s Railway System

© Photo by Rikku Sama/Unsplash
How to Navigate Japan’s Railway System

Photo by Rikku Sama/Unsplash In Japan, a station attendant waits for the arrival of a shinkansen, or bullet train.


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The Japan Railways (JR) Group operates 70 percent of the rail lines across Japan, but there are dozens of smaller private rail companies operating shorter local lines, subways, mountain railways, scenic trains, funiculars, and trams. Japan also has many tourist trains, ranging from rolling restaurants (like Kyushu’s 3.5- hour Coto Cotolaunched in 2019) to luxurious overnight sleeper trains (like the Mizukaze Twilight Expresswith its marble bathroom and deep soaking tubs). These are privately owned and require separate tickets.

Most trains in Japan have normal class and first class called the Green Cars, marked by cheery four-leaf green clovers so the lucky recipients of those tickets can find them. While they are first class, Green Cars never include food or drink. And not all green cars are created equal, so research when and which trains are worth the upgrade. (Personal body height, crowd tolerance, and train journey length are the most likely upgrade variables to consider.) There’s also the uber-lux Gran Class, a fantastic service launched in 2011 on select trains that includes unlimited sake, local sashimi, and perks like eye masks, blankets, and roomy leather seats with a massage function.

You can purchase tickets for all classes at all station counters or at touch-screen kiosks with cash or your credit card. Riders may need to visit the fare adjustment kiosks or offices before leaving the controlled area if they over- or underpay a fare.

The most important thing to know: the categories of train speeds that can be found on all the lines. Local trains are typically the slowest and stop at all stations. Rapid trains skip some stations but cost the same as locals. Ditto for express trains, which typically visit fewer stations. Limited Express Trains typically cost about 600 yen (US$5) more to ride, but get you to your destination quicker.

Are JR Rail passes worth it?

Whether you’re only going from Tokyo to Kyoto and back or planning to tour a big chunk of Japan in a one-, two-, or three-week period, you should consider purchasing a Japan Rail Pass, which offers unlimited rides in the time period of the ticket. They’re only available to international tourists and can offer the most value. That said, do the math before you buy and make sure the cost of the pass does not exceed buying à la carte tickets. Prices for the JR Rail Passes are adjusted every year, but as of April 2021, a one-week pass currently costs about 29,650 yen (US$268) for normal seats and 39,600 yen (US$358) for a Green Car (first-class) pass, which typically offers the most value if you plan to visit two or three destinations. 

As of 2018, it’s possible to buy JR Passes in Japan at four arrival airports and the 11 biggest train stations. This concept has been extended through March 2022 and will likely be renewed for subsequent years, despite some tourists making and being caught using counterfeit passes. Passes can be purchased with proof of a foreign passport, but be forewarned: buying JR Rail Passes in Japan costs nearly $30–$50 more than they do if you buy online ahead of time. The price increase is commensurate to the length of the pass: A one-week JR Pass on arrival, for example, costs 33,610 yen (US$304), $36 more than it would cost to purchase online.

When should I activate the pass?

Many people pick up their JR Pass upon arrival at Narita Airport and activate it for the relatively cheap 90-minute ride to Tokyo on the Keisei Line, which costs around 1,000 yen (US$9)—then, they crash for the night. Although this is doable, it’s not a good use of one of your train days, so make sure to activate your ticket when you’re going a long distance to get the most bang for your buck. If you really want to pinch some yens, use your seven-day JR pass when fares average out to more than $38 a day. 

To activate your JR Pass, you must visit a JR office inside the station. Lines can get long during peak riding hours, so try to activate for the date you want to start it ahead of time. (The JR agents at entrances to the passenger areas can’t activate your pass, no matter how much of a rush you’re in.) Once the pass is activated, show it to the gate agent along with your passport to get in and out of the passenger areas, which often—but not always—have shops, restaurants, and services.

What about tickets for subways?

JR Passes can’t be used for subways. To pass through the subway gates faster, buy a rechargeable, contactless SUICA or IC card at the many kiosks inside stations across Japan. Tapping the card to quickly pass through turnstiles will come in handy when you’re in a rush; the card can also be used in some taxis, 7-11s, vending machines, and many other retailers. You don’t want your SUICA card running out of credit in the middle of rush hour, so make sure it’s topped off with 2,000 yen (US$20) worth of credit, preferably during nonpeak times. The deposit for the card itself costs 500 yen (US$4.50). Your credit will stay on your SUICA card for 10 years, so repeat visitors can use the same card over and over. If you want to cash in your SUICA card entirely and receive your deposit and remaining balance, be aware there’s a fee for doing so: As of 2021, the fee is 220 yen (US$2).

© Photo by Ajay Murthy/Unsplash
Riding the Tokyo subway during rush hour means one thing: crowds.

Photo by Ajay Murthy/Unsplash Riding the Tokyo subway during rush hour means one thing: crowds.

When should I avoid riding the train?

Riding the train during Japan’s notorious rush hour might seem like a fun novelty, but it’s a nuisance to both you and locals trying to get to and from work. If you can, avoid weekday trains from 8 a.m. to 9 a.m. and 5 p.m. to 7 p.m. Friday-night trains between the big cities are also some of the busiest and subject to delays and shutdowns. Sunday afternoons can also see peak ridership when shoppers are carrying bags and occupying more space than usual.

That said, getting caught in Japanese rush hour is a rite of passage and it’s almost inevitable to find yourself in a crowded train at least once. Those who do may relish the story from the experience but will probably take care to avoid it happening again. For women traveling alone who get caught in rush hour, there are many women-only train cars on both subways and some rail lines; trains are often marked in pink.

How do I find the best train maps and schedules?

Google Maps is often your best bet for train schedules. It’s gotten much better in recent years, and like any major public transport system, it lists the time and costs of each train, the stops it makes, and even how busy it is. Inside stations, the leaderboards listing the arriving and departing trains are hard to miss. There are free rail maps at all JR offices and one inside your JR Rail Pass. HyperDia is another English app, and a website that lists all the timetables and schedules of Japanese trains.

How do I ride the bullet train?

Super Express trains are called shinkansen (bullet trains). They’re exclusively operated by JR and always use separate tracks and platforms from the regular trains. Be sure to allocate time to get to the shinkansen platform. In many major stations, it’s a 10- to 15- minute walk from the main ticket offices—and not all stations have shinkansen. In 2017, the SmartEX app launched an English app for visitors seeking to buy tickets, but only on shinkansen trains. The handy app also lets you choose seats and upgrade; it even sends delay and cancellation notifications to your phone. 

The JR Pass is valid on all shinkansen trains, except for the Nozomi and Mizuho trains, which are the fastest trains running on the Tōkaidō and San-yo lines. These trains tend to fill with salarymen, and are typically only 20 minutes faster than other shinkansen trains that depart just as frequently. From Tokyo Station, for example, the Nozomi trains to Osaka take 2.5 hours and depart twice per hour, while other JR Pass–friendly trains depart more frequently and take only three hours. Train geeks (densha otakuin Japanese) and business travelers might want to buy a separate ticket for Nozomi, but the time saved probably isn’t worth the extra cost.  

How do I book seats on a bullet train?

Each shinkansen has reserved-only and nonreserved cars. Reserving seats is free for JR Pass holders, but you have to do so at the JR ticket office or via the app. Many shinkansen trains have a two-three seat configuration, meaning that you may end up sitting between two sleeping salarymen while passing Mount Fuji under bluebird skies. (Remedy this by asking the agent for a window seat with Fuji-san views.) Couples traveling together may want to ask for two seats in the two-configuration side of the train. If there are no seats left, you may be forced to stand or sit separate, so it’s always wise to reserve 24 hours in advance. That said, it’s quite satisfying to score good seats in an empty nonreserved car while watching a queue of gaijin (foreigners) board a crowded reserved-only car. 

© Photo by Manuel Cosentino/Unsplash
Most Japanese trains are as quiet as they are toasty—at times, warm enough to roast sesame seeds. This is how many locals like it.

Photo by Manuel Cosentino/Unsplash Most Japanese trains are as quiet as they are toasty—at times, warm enough to roast sesame seeds. This is how many locals like it.

What about Japanese train etiquette?

Train etiquette in Japan is a big deal. For such a magnificent rail system to work, everyone—including tourists—needs to follow the rules. These rules will be obvious to many: Be kind, be courteous, and avoid direct eye contact so as not to invade someone’s personal space.


Most Japanese people travel luggage-free on trains. Few Japanese travelers carry big suitcases; tourists who do will take up space on trains that seldom have luggage areas, and they may get the stink eye from locals peering out from behind their manga and smartphones. Luggage delivery services like Yamato Transport, known for its iconic black cat logo, are cheap (about $12 per bag), fast (overnight is standard), reliable, and ubiquitous throughout Japan. Even budget hotels can help you with the paperwork to transport your luggage to and from hotels or to and from the airport and most major stations. After all, pushing a giant roller through a busy station is so not kawaii (cute). Do as locals do and ditch your bags.


Boarding trains requires queuing in the designated line spaces on the platform for each car. Even if you have a reserved seat, you will need to queue. If you don’t have a reserved car and you’re trying to score a good seat, you may want to get to the platform early so you can be first in the queue to board early and nab the car’s best seats. 


Use your indoor voice when on the train. If you need to take a call on your phone, make it quick and extra quiet, or exit the car and stand in the areas between cars where nobody will be disturbed or awakened. (When people see pictures of Japan’s dense crowds they often think it must be noisy in these cars, but in many ways, there’s nothing more silent than a crowded train in Japan.) Talk quietly, listen to music via earbuds, or watch a TV show on your tablet or phone at low decibels. Remember, this is a shared public space.

Eating and drinking

Eating and drinking on the train is not only common, it’s expected. (Many locals eat their lunch—often with a beer—on the train and then fall asleep.) If you didn’t get a chance to grab a bento box at the station, consider buying some snacks from the onboard trolley agent who rolls through each car offering sake, beer, and Meji chocolate and bows before departing each car.

Never leave your trash behind on the train like you might on an airplane. There are rubbish bins on the platforms of all stations and riders are expected to clean up after themselves. Leaving trash behind is considered one of the rudest things tourists can do in Japan (ranking aside P.D.A., shouting, and not finishing your meal). If you’ve been reclining, bring the seat back up. But if the window shade is drawn, keep it drawn so you don’t wake other passengers.

Almost all stations have hot and cold vending machines on the platforms, and big stations have 7-11 and convenience stores (konbini) on the platforms so you can go early and shop for a magazine or a snack. In Japan, trains are super punctual and would never depart early, but they come and go within seconds and wait for no one, so it is better to arrive early rather than late.

Train stations across Japan are home to some of the best food and shopping, and many Japanese will allow themselves an extra 30 minutes or an hour to explore and tick off recommended izakaya, ramen joints, and bakeries. 


During the COVID-19 pandemic, masks became obligatory on all trains in Japan. But even before the pandemic, Japan had embraced masks, and they were worn regularly by staff and riders for a variety of different reasons, including allergies, colds, and air pollution. Eating may be less common on trains today than it was before the pandemic, but it’s not uncommon to see someone sneak a snack or a sake under their mask. 

>> Next: Honky-Tonk Tokyo

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