From Japan to Geneva Airport
Unfortunately, there are NO direct flights from major international airports
in Japan to Geneva International Airport. And so, you have to go to there
via major international airports in Europe.
One example: you go to Frankfurt Airport via Narita International Airport
and then Geneva airport from Frankfurt Airport.
From Geneva Airport to CERN
You take the bus number 28 to Hôpital-La Tour (Meyrin). From there, take the bus number 56 to CERN. You can use a free ticket, which is valid for 80 minutes.
reffer to How to get to CERN