Lets start by saying that Japan has an excellent train system that’s fast, clean, efficient and reasonably priced. Train travel in Japan is by far the easiest and most efficient way to get around. The train is so popular that an apartment can cost twice the price if it is within 10 minutes of a train station instead of 20. You can’t even buy a car in Tokyo unless you can prove you have a place to park it. Yes, with 37 million inhabitants in the greater Tokyo area this is like putting all of Canada into one city!
It struck me as we were leaving Shinjuku station one night, that it was similar to exiting a rock concert after a show or sports event after a game, we even looked up with google whether there was a festival going on, or a national holiday, or something… but no, this was just typical and normal people flow which amounts to 3.5 million people every day at that station alone.
It might sound scary, but you know we were quite amazed at how everyone would stick to the left on 
the escalator, there was no garbage or trash left behind, all passengers were quiet and respectful of their neighbors and we had no loud cell phone conversations, no pushing and shoving. We never felt unsafe or uncomfortable. While we say ‘packed like sardines’ the locals say they are like sushi (referring to the rice that are squeezed into a clump).
Many North American cities don’t even have a subway or commuter train. Those that do will typically have one with maybe a few lines in the bigger metropolitan areas. In the greater Tokyo area, you have 30 competing operators offering service on 121 overlapping lines each with their own tickets and routes. You will often have a combination of trains and subways sharing a station, or at least connected via underground tunnels to make transferring easier. Overall, there are 882 interconnected stations and the system delivers over 40 millions rides daily (some are passengers counted multiple times when transferring between lines).
Tickets vary in cost depending on how far you go (you pay when you get off). Usually between $1 and $2. Most people buy a pass, this is a good option for tourists too as you don’t have to figure out the cost of each trip and buy tickets on each transit.
While confusing and overwhelming at first, when you start to see how it works you realize the train transit system is actually quite logical, well documented and organized. As you might expect in Japan!
Local Subways
The metro for example, all have their stations marked with a picture of a subway car on tracks. You’ll then see a circle, which is the color of the line, and within it a letter (or two) denoting the name of the line and a number denoting the station number on that line. For example M12 would be the 12th stop on the Maranouchi line. Each line has its stations numbered sequentially so it’s easy to tell which platform to get onto, you’re either going to the next higher or the next lower numbered station.
Knowing how it works makes navigating pretty easy as all stations have clear markings about which station you are in and which way the tracks go. 
Similarly the stations can be quite large and often under busy streets above ground. Look for a large map as you exit the subway, which shows the layout of the station and all the exits, which are again clearly marked and labeled numerically. There may be as many as a dozen and the underground tunnels are often very long. We found that taking a minute to stop and look at the map and navigating to the right exit could save a lot of time and walking or trying to figure out how to get across a busy street above ground.
Pasmo, Suica, and other Passes
There are multiple flavors of these passes which are like pre-paid debit cards. These are really handy and save time and can be used to pay for your train and metro rides in the city core on all lines. You can also use them at some convenience stores and at many of the vending machines you’ll see at attractions and on street corners. The cards are all pretty equivalent, it really just depends on where you pick them up.
We used the Pasmo cards that we bought at a metro station (one per person). You buy them at a machine and charge them up with an initial amount of at least $10 or 1000 JPY of which 500 JPY is kept as a deposit. Each time you take a ride you’ll see how much is left on your card on a display at the turnstile and as it gets low you can top it up. At the end of your trip just bring it back to the metro station office and you’ll get a full refund for any remaining balance.
The only drawback I should state about these cards is that you pay full fare on each trip (about $2) but you can’t beat the convenience. If you know you’ll be taking a lot of trips on a given day you might consider a metro day pass instead which may be as little as 600 JPY or $6 for unlimited local rides.
Shinkansen Trains
The Shinkansen, or bullet train, is what gets you between the larger cities in Japan. Extremely popular, there is a bullet train leaving every 10 minutes from Tokyo to Kyoto and Osaka (all on the Tokaido line) so you really don’t need to reserve.
This was a surprise to us as we’re used to buying seats well in advance for European trains. Honestly, you don’t have to! We were visiting in the peak of cherry blossom season and spring break for the kids and we still got seats on the next train or the one after never waiting more than 30 minutes. We generally picked the later train ourselves, as we were not sure we’d find the platform any faster.
The trains themselves are all high-speed bullet trains but depending on the number of stops they are classified into three different speed categories. On the Tokaido line the Nozomi is the fastest and makes it from Tokyo to Osaka (about 500 km) in just over 2 hours with only 5 stops. The Hikari and Kodama trains do the same route but stop at more stations and thus add more time to the route.
There are two classes of cabins on the trains, the green cars which are first class (a 2 seat and 1 seat configuration) and the normal cars which are economy class (a 3 seat and 2 seat configuration). All first class seats are reserved, but in economy you have both reserved seats on some cars, and non-reserved (grab a seat anywhere if you can) cars. We found the economy seats extremely comfortable with lots of legroom and we didn’t find that first class was worth the premium price of about 1.5 times the regular fare. We did opt for reserved seats as the one time we didn’t we had a hard time getting seats and had to sit apart. This has only a small premium ($10 extra on a 130$ fare from Kyoto to Tokyo).
Japan Rail Pass
You’ll find many sites that tell you this is a must before you go to Japan, and they tell you that you must purchase a voucher from them before arrival and exchange it when you get to Japan for the pass. Do your math on this one as we found that for us, it was not going to work well and would limit our flexibility. A one-week pass at the time of our trip was $270 and this was about the equivalent of the fast train on a return trip from Tokyo to Osaka. Since we were staying almost two weeks, we would have needed a two-week pass and this would add up to more than what we’d pay for individual tickets.
There are also limitations with the pass. You can’t take the Nozomi (fastest train) and you can’t use it on the local trains or subways. Overall we paid $135 each for our reserved seats on the Nozomi trains and about another $50 each for lots of subway trips on the Pasmo card. We did take limo shuttles to and from the airports and our hotels often offered free shuttles to and from the rail stations.
The JR does have a circle line in Tokyo that might get you close to the sights, but the convenience of taking all the other lines if you need them make the more general pass a worthwhile investment and will save you lots of walking. We were also amazed at how Google Maps could help route us through the trains and subways to get to our destination (and it doesn’t have a JR pass only option).
Taxis
Tokyo is insane for taxis. Expect a $300 fare from Narita Airport to Shinjuku and perhaps a $100 fare to Haneda Airport. The cities gridlocked traffic makes these the most expensive and least efficient ways to get around. We fared better in Kyoto where some of the attractions were further afield and a $10 taxi ride saved us 1/2 hr or more on train transfers but when it comes to Tokyo, we would often out walk the taxi’s we saw on the streets.
Additional Information
Be careful around rush hour on the subways, as some of the lines have instituted women only cars. This is meant to protect women from the close contact of getting squeezed into the cars like sushi. Men, have also requested to have their own men only cars for fear that they may be falsely accused of inappropriate touching. When you’re squeezed into a car like sushi, even lifting your hand to scratch your nose might be misinterpreted if you are too close to the passenger next to you (a actual real life case which was told to us where someone had to spend 2 weeks in jail for such an accusation). Some men even ride the busy cars with both hands up high holding the railings to keep them in sight!
There are also some designated seats (clearly marked) that are reserved for elderly or injured persons. Make sure to give these up if you see someone that might need the seat if you happen to be in one. Also, do mind your manners, there is often a hushed silence on the trains and it’s somewhat taboo to be loud or boisterous. We didn’t see anyone talking on their cell phones, all were quiet and respectful.
Google routing was excellent and it would always direct us to the closest stop and give us the shortest route.
Many of the trains had free WiFi, you just had to register with an email, but it was easy to do and the coverage was good.
Related:
- A self-guided tour in Japan, not as Difficult as It Sounds
- Visiting Tokyo at Cherry Blossom Time
- Top Places to See in Kyoto, Japan
- Top Attractions to See in Osaka
- Street Food and Other Traditional Dishes to Eat in Japan