As you probably know, the whole downtown area of Tokyo is encircled by JR's (Japan Railway) train line called Yamanote Line. And most of the major stations like Shibuya, Shinjuku, Shinagawa and Akihabara are on this line, and most of these major stations have subway stations nearby, so you can travel further to any area in Tokyo by taking connecting subway lines.
If you can't find out which train you should take to get to your destination, just ask someone at the train platform service area. You don't have to be fluent in Japanese, you only need chotto(little bit) of Japanese.
For example, if you want to make sure if the train you will take goes to Shinjuku Station, just ask by pointing at the train.
"Sumima-sen, Kono Densha, Shinjuku ni iki-masu ka?"
(Excuse me. Does this train go Shinjuku?)
This phrase is not grammatically correct in Japanese, though it is easy to say and you can avoid misunderstanding from Japanese people.
On weekdays, most of the trains run every 2 to 5 minutes. So, don't panic even if you miss the train, while trying to find out if this train was the right one. It won't be too long until another train comes.
And here's another useful tip....
Even if you understand how to take trains, it is sometimes troublesome if you can't find out how long it would take to get a destination. Downtown Tokyo is bigger than you expect. You can never figure out how long it will take unless you understand the actual size of the city. In this case, you can find out travel times with this method called "the rule of 2 minutes".
The Rule of 2 Minutes
Traveling time between, station to station, by train in downtown Tokyo is about 2 minutes on average. It sometimes takes 3 minutes, but I always figure it for 2 minutes, as a rule of thumb. So, you can find how long it will take by the calculation below:
Number of Stations x 2 minutes
For example, let's suppose I was going to meet a friend at JR Tokyo Station. The nearest station from my place is JR Nippori Station, so I am to take JR Yamanote line from Nippori to Tokyo. From Nippori to Tokyo, there are 6 stations. So, I can calculate the supposed traveling time like this;
6 Stations x 2 minutes = 12 minutes.
Plus, I consider extra time, maybe 5 times for walking toward a platform or waiting for train etc.
12 min + 5 min = 17 min. So. I figure out I need at least 17 min. to get to Tokyo station from Nippori station.
Following this example, you can find the length of time you need by the proceeding calculation.
If I go to Shinjuku station from Nippori, there are 10 stations, the calculation goes like this;
(10 stations x 2 min ) + extra 5 min = 25 min.
I can figure out that I would be able to get Shinjuku from Nippori in 25 min!
You can use this calculation for subways too.
If you have to change trains, you need to add more extra minutes, though, the rule of 2 minutes works for any cases.
Note: *If you are a careful person, you can change it to "the rule of 3 minutes".
By understanding this, you can become an expert in navigating the transportation systems in Tokyo.