Trains are the best. From bullet to local. You could do only trains (and very reliable perfectly synced buses, and a bit of walking) and get (almost) everywhere you’d want to go.
More details on the JR Pass below. I’ve usually gotten one pass or another, but I am very unlikely to get another 1–2–3-week standard all-you-can-ride pass, because you really have to cover a lot of ground quickly to make it worth the money. Also heard the cost is going up later this year (2023).
Road trips also fun: If you have a group and want to rent a car, that can be enjoyable, too, and very convenient in rural areas — though car rentals, fuel & toll roads are expensive, speed limits quite strict, and distances a hell of a lot farther than they seem on the shinkansen. Various short term car rentals also available; none are that cheap.
For car rental, bring an international drivers permit: You can get one for $20 in 15 minutes at AAA offices across the US. Just take your valid license and two passport photos with you. Some Japanese car rental companies say they will accept certain countries’ licenses, but they could hesitate or refuse; they’re more comfortable with the international permit.
How to decide: Your transportation strategy will mostly depend on how much distance you plan to cover in what period of time. 90% of the time, the train is best (cost, stress, ease). For farther cities and towns, local flights can be very well priced and much faster (note: cheaper airlines can have the usual budget airline luggage restrictions).
Renting a car is advised if you have specific destinations that can only be accessed by car, like some mountain lodges, far suburbs, specific rural areas (out of reach of train lines), or small towns across Hokkaido. I love being able to just go off the main paths a bit.
Other domestic options: taxis and flights
Taxi tips: They are super professional and nice (and can add up).
- They are not that expensive for short trips ($10–20 for 10–15 minutes at a normal flow). Taxis for long distances will get very expensive.
- Follow the order or queue. At a station or taxi point, go to the front loading spot where they’re lined up and obediently wait your turn.
- Taxi doors (back left) open and close automatically: don’t force the door!
No rideshare? I think Uber is only legal in rural areas where public transportation is too limited. Otherwise I believe it’s totally banned. It looks like there’s another service or two (as recommended by Google Maps) but I could never get it to work and didn’t look into it.
Domestic flight travel in Japan is super easy/quick/reliable.
There are a handful of small airlines that can offer pretty good deals. And all function pretty well, other than perhaps you're needing to shuffle over to a less central part of the airport. Note luggage restrictions, as overage fees can be expensive. That said, if you end up buying a heavy statue or box of cantaloupe while traveling, you can almost always have it easily and cheaply mailed overnight rather than carry it back yourself, to any domestic destination, or even to the airport for easy pickup.
The regular airlines also offer good domestic flights, though they don’t seem as cheap as the smaller airlines. United / Star Alliance (same as TAP, Lufthansa, etc) has some good domestic flight options. On Star Alliance you can book good “saver” domestic flights. Also check for deals where you could add a domestic flight on top of your round-trip international trip.
Train/subway strategy in and around Tokyo: The Tokyo subway system is fantastic, but there’s a good amount of strategy to getting good at it.
- Load a SUICA/PASMO card directly onto your iPhone or Apple Watch from Wallet, if you have an international Mastercard. I’d read that for international cards only Mastercards work, and that was true for me. You can also use it to touch-pay at loads of shops.
- Or buy a physical SUICA/PASMO/IC card and reload it at any station, using cash only. Buying the physical card in Japan, rather than online, will ensure it’s registered in your name. (Note: You don’t need to use a card at all if you are taking JR trains on a regular unlimited JR Pass, but if you transfer onto non-JR it’s nifty.)
- Remember there are a good number of different companies. The routes and schedules are synced well, and you can almost always use the same card to pay, but the experience can be pretty different, and often you’re walking from one train company to another within a station, or going in/out of turnstiles for different ones. It can be quite a walk.
- For trip planning, there are many apps, but the most functional seem to be in Japanese (language). Various apps are geared towards foreigners but seem kind of bootleg, though they are getting better. Set them up in advance.
- Google Maps does pretty well, in almost all places, but just be careful and re-run your options to learn what is and isn’t appearing. It can occasionally be wrong on smaller train lines, like knowing which train stops where, between every-station, rapid, special rapid service, on weekdays vs weekends. (There might be better apps.)
At night, latest, take the second or third to last train: Subway lines stop running at around midnight, so you have to make sure you get on that last train, the shuuden, or your taxi ride home will be prohibitively expensive. In recent years, there have been significantly more train delays. Heading out of the city, it seems like they try to line up the next trains that a lot of people are transferring onto, but you don’t know that for sure, so you end up nervously waiting to arrive at your transfer station, then sprinting to the other platform, hoping it’s waiting for you. My advice: take the second or third to last train for the night, or stay over at a more centrally located friend’s house.
Local/express trains & skipping stations: For trains heading outside of Tokyo into the extended “suburbs” (they’re still very densely populated cities), there are local (futsuu) /express (kyukou) / rapid express (tokkyuu) trains. Both express trains will skip a bunch of stations, so make sure your stop isn’t one of them. Study the maps (which dots/lines pass through). Many trains have electronic signage, too. Local and express trains will stop on opposite platforms so people can transfer from one to the other, but most of the announcements are only in Japanese. Again, study the maps. :)
Follow the train line traffic instructions: Traffic lines drawn on the train platform are there to direct people to form lines for each type of train. Folks take the lines very seriously, so don’t skip ahead, or butt in from the side.
Double-check your destination: Google Maps also requires you know exactly where you’re going. Many places can have the same name: XX-town-name can be unrelated to XX-station… you have to add the word “station” (or eki) or you could end up in a totally different place.
Take advantage of luggage lockers: There are lockers of various sizes in train stations, for if you are traveling and want to explore and return to the station to retrieve your luggage. Not super cheap (500–800 yen) but can be a life saver. Just don’t forget which set of lockers you used! (The lockers went away for about a decade post-2001 but have almost entirely returned.)
Don’t follow Google Maps or other apps mindlessly, or it won’t turn out well. Think strategically. The apps and Google Maps don’t get to the best of the strategy, like
- where to stand on the platform to get off where you want to (you could end up at almost a different station, for longer trains like the Yamanote line that circles the city)
- whether to wait for the next train for a seat
- whether you could walk one station over instead of transferring later
- ladies cars: The rush hour female-identifying-only cars (in the front of the train) are really pleasant.
- factoring in your JR Pass options
Pro tip: If you have JR Pass, since it’s free, even when going from one side of Tokyo to the other, hop on the nicer trains, like the extended Narita Express or special limited request trains. Sooo much cushier!
Google Maps and other apps won’t help you maximise your JR Pass, since only foreigners get them. For most riders, such short rides on the nicer trains would be cost-prohibitive and not worth it.
Country-wide & JR Pass
Consider the JR Pass if you’re covering a lot of ground: If you’re traveling around a good distance in a short time, the all-you-can-ride JR Pass can be a good deal and also just make for ease of travel, and only foreigners/non-residents get to enjoy them.
JR Pass is not all-inclusive: “JR” is actually a different company depending on region, so the pass is a collaborative effort between the companies. Also, watch out for non-JR train routes, whether in Tokyo or in a rural area, including many non-JR trains to popular destinations!
JR Pass excludes the fastest shinkansen betwen major cities: This doesn’t seem like a big deal, but you might end up transferring once or twice more than you would otherwise have to (to get the second fastest route) and also the oversize luggage pieces of the many, many foreigners on those not-fastest trains become a bit of an obstacle course.
Use another app like Japan Travel (not google maps) to determine best route if you have a JR Pass: You have to rule out the fastest shinkansen and you might also want to prioritise JR routes to save money.
You can buy the pass online and pick it up at the station: But the passes are ~15% cheaper when purchased from outside Japan. For decades the country-wide JR Pass could only be purchased before entering Japan, but there is a trial period for domestic sales that keeps getting extended, since 2017. However, now Japanese citizens (the ones who qualify for JR Passes, as non-residents with proof of living abroad) cannot buy them in-country.
One, two, or three weeks: JR Passes Plan strategically for your length of stay depending on rail pass & where you plan to go while you’re around. Or if you don’t want to even think about it, then, sure, just get a JR pass for the whole duration of your stay. It is nice to just travel (almost entirely) freely for one flat rate, and sometimes you can get a cushy train even for cross-Tokyo travel.
If you’re traveling serious distances, this will make the cost of a JR Pass worth it. It’s also nice to be able to get on/off, not worry about missing the train you booked, book at the very last moment, etc.
Also consider the regional passes! More limited regional passes have more flexible rules. And can be the very best deal, most cost effective, depending on your intended route. Like the NEX pass (for Narita airport to city and back, though max 14 days of validity) and the JR East Pass, which is good for four nonconsecutive days on the whole main island from Tokyo north (I think still). You can buy those and others at the airports or major train stations.
Shinkansen: bullet train
Be discerning about your train routes: You can book easily by scanning your JR Pass QR code at machines. But also those green windows/counters (midori no madoguchi) can handle requests quickly, and nowadays the representatives are really good at spitting out your best strategic options in English on slips for you to compare and decide.
Free and reserved seats: There are two types of seats on the bullet train: reserved seating (shiteiseki) and free seating (jiyuuseki). If you’re traveling on a JR Pass, you can do either. You can walk up to the JR counter (green offices in stations) and ask for a shiteiseki for your route, even minutes before the next train. It can nice to know where you’re going to sit.
When not using a JR Pass, free seating is cheaper, but you’ll need to figure out which cars are for free seating. Reserved seats may be the way to go if you’re traveling at a busy time of year, or around rush hour. The shinkansen accommodates a lot of commuters and vacationers.
If you have big luggage (and sadly didn’t ship it): If you’re toting check-in size luggage, you have to reserve special luggage rack. This could restrict which trains you can reserve, if it’s a busy time and others have nabbed those spots (most likely foreigners).
Don’t spend all your time in Japan on a train: If you have a nationwide JR Pass, finding out how far can you get at >300 km per hour can be tempting. But rather than try to get everywhere, and spending lots of time on trains, I’d suggest to move a little slower, see a bit more of each place. (How many castles and shrines and ancient temples last hit by lightning and rebuilt in 1987 are you going to be able to keep straight in your head later anyway?)
Be strategic: To maximise without rushing like a nut, you could also take a JR Pass far south or far north, stopping along the way, then stay a few days at the final destination and take a cheap domestic flight back. You could also pair the JR Pass with the airport NEX pass: don’t activate/start your JR Pass duration immediately, unless you’re traveling far on day 1 upon arrival.