If it is your first time to visit Japan, and you have only a week in Japan, then consider to take so-called Golden Route. This route visits Tokyo, Mt. Fuji or Nikko, Kyoto and Osaka, in this order or vise versa. You stay overnight in large cities such as Tokyo, Kyoto and Osaka. And take day tours.
For those who do not know much about Japan, then take a tour for a week. Tours are available from Narita International Airport or Kansai International Airport.
Model Itinerary of Golden Route in one week
This itinerary starts from Tokyo. You can start from Osaka and end in Tokyo.
Day 1: Arrival in Tokyo
You land at either Haneda Airport or Narita Airport. You stay in Tokyo for sightseeing in Tokyo. Depending on the time you arrive in Tokyo, you may take a city tour, or enjoy an activity.
Day 2: One day in Tokyo
Take a day-tour in Tokyo. Visit Asakusa Sensoji Temple, Imperial Palace, Harajuku, etc.
Day 3: Mt. Fuji or Nikko
You take a day tour to Mt. Fuji or Nikko. Stay overnight in Tokyo.
Day 4: Move to Kyoto
Take Shinkansen bullet train from Tokyo to Kyoto. You can make a stop over at Nagoya. But many people skip Nagoya.
Day 5: One day in Kyoto
Take a day-tour in Kyoto.
Day 6: Osaka tour or Nara tour or one more day in Kyoto
You have choices. Take a day-tour in Osaka. Alternatively you visit ancient capital Nara, or you can spend one more day in Kyoto.
Day 7: Departure from Kansai Airport
If your hotel is in Kyoto or Osaka, take train or bus to go to Kansai International Airport. Private transport is also available from Kyoto/Osaka to Kansai International Airport.