You can take a plane between most major Cities in Japan.  Like everywhere else you will need to get to the airport, check in at least an hour before the flight, take the flight, and then get from the airport into the city center.  If you are going to one of the extreme ends of Japan (North or South), this makes sense as the time to get between Tokyo and those locations can be shorter by plane then by Shinkansen, taking into account all the waiting you will be doing at the airport.  Intercity flights in Japan are usually priced comparable to Shinkansen tickets and for some destinations are cheaper.  

The main con to flying is the need to go through security and wait for the flight to take off and then get from the airport back to the city when you arrive.

The Train is the most common way to get around Japan.  If you will be travelling to more then three cities then getting a JR rail pass may make sense.  You can also use your Suica card to board and ride most trains making them very convenient.  Most larger cities have multiple rail companies and subway lines connecting most parts of the city together.  The trains also run on time and to schedule so you can trust the timetables for each train.  There is no security for trains and you can hop on and off them as needed.

The main con for the train is that they tend to stop running at midnight and don’t start until 5AM.  So if you are out partying you may not have a ride home.  Also the trains in Tokyo during rush hour and the last train of the night can get quite crowded and you may be pushed into the train car.  Also in cities like Osaka, Kyoto the trains may not go near all the major attractions and you may need to grab a bus or a taxi to get you the last few kilometers to where you want to go.

When you ride a train in Japan expect to get lost and make a mistake it happens to everyone.  Just get off when you realize and cross over to the other platform and ride back.  One trick we developed quickly was to use Google maps to get around as it tells you what platform to get onto and when the train will be there.  Trains share platforms and everyone takes a wrong train in Japan especially Tokyo.

When we traveled to Japan for 3 weeks we bought a 14 day JR Rail pass.  We used it to buy multiple Shinkansen tickets and we used it around all of the major cities on the JR lines.  Please note that the passes only work on JR rail trains and buses.  If you get on a private rail line like the Odakyu or Tobu lines the rail pass will not work and you will need to use your Suica card, the same holds true for the Tokyo Metro.  If you are going to be in Tokyo you can get day passes for the Tokyo metro.

If you get a JR rail pass one thing to remember it starts at midnight the day you activate it and it ends at midnight the day it expires.  If you by a 7 Day Rail pass and activate it on Monday.  It will start at Midnight on Monday and be good until Midnight on Sunday/Monday.  So if you take a train at 11:45 on Sunday and it arrives at your station at 12:10 AM Monday you will need to pay for that trip as you were on the JR system after your pass expired.  You can also activate your pass a few days in advance.  So you could activate it on Friday for the following Monday and have it ready for you.  This is especially helpful if you are going to take a Shinkansen during the busy season and want to reserve a seat.  Go to the customer service center on Friday activate your pass and get your reserved seat for the 7:10 Shinkansen from Tokyo to Kyoto.

Most of Japan has buses it is very convenient to get those last few kilometers from a train station.  You can also take the mus into more rural areas of the country.  Japan also has an overnight bus that runs from Tokyo to a lot of the major cities such as Osaka and Sapporo.  You can pay for buses with your Suica card, but you need to check and see if the bus is a swipe when you get on bus, or a swipe when you get off bus.  You will know this based on where you enter the bus, if you enter at the front you swipe when you get on, if you enter in the middle you swipe when you get off (at the front of the bus.)  Buses like trains can get crowded.  We took a bus to Tsukiji fish market that was standing room only and we were packed in like sardines.  The buses are clean and just as efficient as the train system in Japan.

The main con to buses is how long it takes to get from where you are to where you want to be.

Most cities have taxis in Japan.  You can use an app to hail one or just hold your arm out as one drives by.  They will take you where you want to go and they all take the Suica card.

The main con to taxis are they are more expensive.  A 240 Yen train ride across Tokyo from Shinjuku to Asakusa will probably be closer to 5000 Yen by cab.

As of posting this article, Lyft does not operate in Japan.  Uber operates but only in the Major cities and is a privately owned company that uses the Uber app (think taxi).  I did price Uber rides to see what the cost would be, and where a taxi might be 5000 Yen an Uber was going to be 7000 or more.

You can rent a car in Japan, but you will need an international drivers license or an armed forces of Japan drivers license. I would only recommend doing this if you are going out into the country side.  Driving in Tokyo is not for the feint of heart and with congestion charges and toll roads could get quite expensive.  One thing I noticed in Tokyo was the lack of public parking or parking at AirBnB’s or hotels.  

For our entire trip we used trains and buses to get around.  We never felt the need to take a taxi or rent a car.  We were prepared to take a taxi if we were out late at night, but usually we started early and got tired around 11PM and headed home.

Cheers,

Dave…