If you only visit a single museum in Tokyo, it should be the Tokyo National Museum with the world’s largest collection of Japanese art. Here you will find ancient pottery, samurai armor and swords, wood block prints, kimonos, sculptures and more. The main focus should be the Japanese Gallery (and you can only visit this if you want). This gives the best overview of the history of Japan. I would start downstairs on the main floor at the adjacent (you don’t have to leave the building) Heiseikan that has the Japanese Archaeological Gallery full prehistoric artifacts/history and then go back to the main gallery and upstairs to see the rest. With more time you can see the Toyokan that has a big collection of asian arts or the Gallery of Horyu-ji Treasures. There are special exhibits at this museum as well so you can check those out on line ahead of time.
Hours
Monday: ClosedTuesday: 9:30 AM – 5:00 PMWednesday: 9:30 AM – 5:00 PMThursday: 9:30 AM – 5:00 PMFriday: 9:30 AM – 8:00 PMSaturday: 9:30 AM – 8:00 PMSunday: 9:30 AM – 5:00 PM