Japan Rail Pass can be used on the Railway lines that go from the main airports to the major cities in Japan. You can activate your Japan Rail Pass in the appointed offices at the airport. The JR travel service centers and ticket offices are mostly located next to the entrances to the platforms.
If you are planning to arrive at Haneda Airport, you can take the Tokyo Monorail which goes to Hamamatsucho station. If you are going to land at Narita Airport you may use Narita Express to go to Tokyo, Shinagawa, Shinjuku, and Ikebukuro stations. From the Kansai International Airport, you can catch the limited express Haruka train that will take you to Osaka or Kyoto.
If your plane lands at Fukuoka or Nagoya airports you will need to get to the nearest stations to exchange and activate your Japan Rail Pass.