If you are arriving by plane, check beforehand if the airport is Narita (NRT) or Haneda (HND) as they are at completely different locations. A majority of international flights arrive at Narita, which is about 60 kilometers east of central Tokyo. Most domestic flights as well as an increasing number of Asian flights touch down at Haneda which is more conveniently located just south of central Tokyo.
From Narita Airport -
Narita has two terminals but each one has its own train station and bus stop located nearby at the arrivals area.
The bus stop is at the ground floor (where the arrivals area is) and you'll find the ticket counter in front of you with the orange signs.
The trains depart from the underground so it's a bit of a walk, about 10 minutes.
Follow the signs downstairs; escalators and elevators are available.
Trains originate from Terminal 1 and stops at Terminal 2 before heading to the city, where as buses start from T2 and then picks up passengers at T1.
Update : A new Terminal 3 opened on April 2015. Jetstar, Jeju Air, Spring Japan and Vanilla Air has now been allocated to this new terminal geared for LCCs (Note that Peach Aviation will continue to depart from Terminal 1). Most buses stop directly at Terminal 3, while train users will have to use the Terminal 2 station which is about a 15 minute walk away, thus plan on allowing some extra time for this move.
1) JR operates the all-reserved Narita Express (NEX). If you will be travelling with the JR Rail Pass, then this will be the better option as you do not need to pay anything additional.
There are departures every 30 minutes withe some trains going to Shinagawa (70 minutes) and Yokohama (90 minutes) while other trains head to Shibuya (80 minutes), Shinjuku (90) and Ikebukuro(95). All trains stop at Tokyo (60 minutes from Narita).
Holders of a foreign passport will be able to get a discounted ticket for 1,500 yen - a real bargain since ordinary tickets cost more than 3000 yen. Unfortunately there are no discount of this kind from the city heading to Narita.
N'EX TOKYO Direct Ticket
2) Keisei also operates trains that are a bit faster and inexpensive depending on your destination.
The Skyliner is the fast train reaching Nippori (for transfers to the JR Line) in 36 minutes and Ueno in 41 minutes. The fare including the compulsory reserved seating is 2470 yen. Once you enter the station, go down the first set of stairs, marked in violet.
The Access Express makes more stops and comes with non-reserved seats that are less comfortable than the Skyliner. These trains go directly towards the Subway Asakusa line and Keikyu Line meaning you'll have direct access to Asakusa, Nihombashi (about 60 minutes), Ginza, Shimbashi, Shinagawa and Haneda Airport (100 minutes/1800 yen) The down side is that these are commuter trains so it can get very crowded during the rush hour. They have no luggage space except for some limited overhead space only large enough to hold carry-in sized suitcases or backpacks.
They depart from a separate section of the platform so go down the second set of stairs marked in orange.
Again, there are discounts for holders of foreign passports so check here.
Airport Limousine offers buses to the major stations and hotels within the entire Tokyo/Yokohama Metro area.
This might be the most comfortable option especially you have lots of luggage and you want to avoid the hassle of going up and down stairs at the stations.
A trip to Tokyo station for example will take about 100 minutes and 3100 yen.
An early morning arrival on a weekday might mean you're going right into the morning commute, and in general the buses take more time than the trains.
Just launched recently, the Limousine & Subway Pass includes unlimited travel on ALL of Tokyo's subways and may be worth looking into.
The inexpensive way:
Running every 20 minutes, there is also a bus going to either the Yaesu side of Tokyo station or the Ginza area (close to Yurakucho Station) The buses are just 1,000 yen! There are two operators of this economical buses, which are just as clean and efficient as the Airport Limousine.
" Access Narita" Co-operated by JR and Be-Transe
"Tokyo Shuttle" Operated by Keisei
Both of these buses depart from the same platform, but "Tokyo Shuttle" requires you to buy a paper ticket at a counter first while you can pay the driver directly for the "Access Narita".
For the trip back to Narita, Access Narita leaves from quay 7 immediate outside the Yaesu South Exit of Tokyo Station. They are much easier to find then the bus stop for the Tokyo Shuttle or the Airport Limousine. Again, you simply pay as you board the bus.
These budget services seems to have become extremely popular; now many buses are running at full occupancy. The buses originate in Terminal 3, next stopping in the order of T2 and T1 before heading to the city; passengers coming out of terminal 1 may find it hard to find available seats.
Exchanging your vouchers for the JR Rail Pass
You can do this at the JR EAST Travel Service Center at the airport. These are on the basement level at both the Terminal 1 and 2 stations. During the late afternoon when many flights from the US arrive, the lines can get a bit long. However once you get into central Tokyo, finding the places to exchange your vouchers can be somewhat tricky. You can choose a future date for the timing when you want to start using the pass, so even if you don't have intentions of using the pass on the day of arrival, we would recommend for you to get the validation done while you are at the airport.
You will have to fill in a form with your name and passport number. If the lines aren't too long, the staff might let you book one or two train tickets, but if not you can reserve your seats at any of the counters marked in green ( "Midori no Madoguchi") that you will see in most stations.
The vouchers you received at home must always be exchanged for the actual pass itself. Even if you don't have plans to use the pass for the next few days, it is best to get this done at the airport. The clerk will ask you the specific date you want to start using the pass.
The hours and locations of all JR Rail Pass activation points can be found here : http://www.japanrailpass.net/en/exchange.html