If you are doing an international flight and notice your ticket says you have a stop in TOKYO, you are probably thinking, cool you have a few hours down you'll jump in a cab right into the city. Well unfortunately it is more complicated then that.
If you have a international stop over and your ticket says TOKYO, the airport you are using is Narita International Airport. Narita Airport is some 60 km outside of Tokyo.
The reasons you don't want to go all the way out to Tokyo on a short layover:
Immigration and Customs clearing can take upwards to one hour. Then you will need to factor in time for currency exchange and purchasing train tickets.
A train can take 1 - 1.5 hours just to get into Tokyo, then another 15-30 minutes to travel within the city.
On your return to the airport you have to go through multiple security checks (2-3 different ones), then you have to go through exit immigration lines at the airport.
So in all, you have to factor: getting into Japan (immigration&customs), then transportation into Tokyo, transportation within Tokyo, then some time to actually sightsee or do something, then all of that multiplied by 2 since you have to go back to the airport, then back at the airport you have to factor time for all the security checks and exit immigration. Don't forget that for international flights passengers have to be check-in and onboard at a certain time before the scheduled departure time.
It can be upwards of five hours of just going through all these steps not including any time to actually sightsee in Tokyo, not to mention how much time you lose if you get lost.
You can certainly see that if you have a short layover, going all the way out to Tokyo might not be the most practical. I'm not saying you can't go all the way out, if you feel you can make it then plan accordingly.
Now you're not forever stuck to the airport.
What can you do?
Lets say you did have a few hours laying over in Narita Airport, and wanted to get out. Say 5-6 hour layover, or that you are overnighting in the area and need to catch a flight the next morning.
First is if you require a visa or not to enter Japan.
If you come from most major developed countries, then you do not require a tourist visa to sightsee (this is known as Visa-Waiver), you just need your passport.
See here from the Japanese Immigration website to see if your country is listed.
Note: You have to be Citizens of these countries, not Permanent Residences.
*I'm not going into detail on how to get a visa if you need one, I'm not an expert on that matter, see the Japanese Immigration pages on how to get one if you need one.
Most people who have a short layover in Narita Airport and want to get out of the Airport, visit nearby Narita City.
Narita City has a nice temple and offers various shopping not found in the airport.
There is a large shopping complex called the AEON Shopping Center. Aside from the temple in Narita, it is a large tourist attraction especially for those on layovers at Narita.
Transportation into Narita City from the airport is pretty easy.
By train the Keisei Limited Express and JR Rapid Airport Narita connect to Narita City.
Keisei trains run about every 15-20 minutes from Narita Airport and costs 250 yen.
JR Rapid train departs once an hour (usually at the top of each hour), and costs 230 yen.
Travel time to Narita Station from the airport is roughly 10 minutes.
Remember which terminal you go on the train at. There are two terminals at Narita Airport, each with its own train station.
DO NOT TAKE THE JR NARITA EXPRESS OR KEISEI SKYLINER TRAINS. These are more expensive to ride, and most times the NEX doesn't even stop at Narita.
Remember which terminal your airline is located, there is a train station at Terminal 1 and a train station in Terminal 2. The train station for Narita City is simply Narita Station (Keisei Narita if you use Keisei Railways).
Also, buses from the nearby hotels in Narita provide shuttle service.
Japan Ministry of Foreign Affairs (visa waiver information)
Narita City Website (sightseeing information as well)
Naritasan (famed temple in Narita)
Narita International Airport