Here are the top ranking universities in Japan:

1. University of Tokyo - consistently ranked as one of the top universities in Japan and the world.
2. Kyoto University - known for its strong research focus and traditional cultural setting.
3. Tohoku University - a comprehensive research university with a strong emphasis on science and technology.
4. Nagoya University - a leading research institution with a focus on engineering and natural sciences.
5. Tokyo Institute of Technology - a top-ranked science and technology university.
6. Osaka University - a major research institution with a strong focus on medicine and engineering.
7. Hokkaido University - a comprehensive research university with a strong emphasis on natural sciences and engineering.
8. Kyushu University - a top research institution with a focus on interdisciplinary studies.
9. Keio University - a prestigious private university with a strong emphasis on business and law.
10. Tokyo Medical and Dental University - a leading medical and dental university in Japan.