Best Universities in Japan for research Based on THE World University Rankings 2018 |
| Rank | University | Score for research |
| 1 | University of Tokyo | 85.2 |
| 2 | Kyoto University | 78.6 |
| 3 | Osaka University | 57.6 |
| 4 | Tokyo Institute of Technology | 52.9 |
| 5 | Tohoku University | 50.6 |
| 6 | Nagoya University | 47.2 |
| 7 | Kyushu University | 40.7 |
| 8 | Hokkaido University | 40.2 |
| 9 | University of Tsukuba | 35 |
| 10 | Tokyo University of Science | 24.9 |
| 11 | Keio University | 23.2 |
| 12 | Tokyo University of Agriculture and Technology | 22.6 |
| 13 | Waseda University | 22.1 |
| 14 | Yokohama National University | 21.8 |
| 15 | Tokyo Medical and Dental University (TMDU) | 20.5 |
| 16 | The University of Electro-Communications | 19.8 |
| 17 | Hiroshima University | 19.6 |
| 18 | Kobe University | 19.3 |
| 19 | Nagoya Institute of Technology | 18.7 |
| 20 | Tokushima University | 18.1 |
| 21 | Chiba University | 17.7 |
| 22= | Kanazawa University | 16.7 |
| 22= | Toyohashi University of Technology | 16.7 |
| 24 | Okayama University | 15.4 |
| 25= | Kyoto Institute of Technology | 13.9 |
| 25= | Osaka City University | 13.9 |
| 27 | Kumamoto University | 13.6 |
| 28 | Tokyo Metropolitan University | 13.3 |
| 29 | Mie University | 13.1 |
| 30 | Ehime University | 13 |
| 31= | Nagaoka University of Technology | 12.8 |
| 31= | Tokyo University of Marine Science and Technology | 12.8 |
| 33= | Nagoya City University | 12.5 |
| 33= | Shizuoka University | 12.5 |
| 35 | Juntendo University | 12.4 |
| 36= | Nagasaki University | 12.3 |
| 36= | Osaka Prefecture University | 12.3 |
| 38 | Kyushu Institute of Technology | 11.9 |
| 39 | Saitama University | 11.7 |
| 40= | University of Hyogo | 11.6 |
| 40= | University of Toyama | 11.6 |
| 42 | Saga University | 11.3 |
| 43 | Kagawa University | 11.1 |
| 44 | Kagoshima University | 10.9 |
| 45 | Gifu University | 10.8 |
| 46= | Niigata University | 10.7 |
| 46= | Sophia University | 10.7 |
| 48 | University of Yamanashi | 10.5 |
| 49 | Iwate University | 10.4 |
| 50 | Yamagata University | 10.3 |
| 51 | University of Fukui | 10.2 |
| 52= | University of Aizu | 10 |
| 52= | Meiji University | 10 |
| 52= | Shimane University | 10 |
| 55= | Nara Medical University | 9.6 |
| 55= | Tokyo City University | 9.6 |
| 57= | Kindai University | 9.4 |
| 57= | Kochi University | 9.4 |
| 57= | Shiga University of Medical Science | 9.4 |
| 60= | Toyo University | 9.3 |
| 60= | Yamaguchi University | 9.3 |
| 62 | Utsunomiya University | 9.2 |
| 63 | Akita University | 9.1 |
| 64 | Ritsumeikan University | 9 |
| 65 | Shinshu University | 8.9 |
| 66= | Chuo University | 8.8 |
| 66= | Kitasato University | 8.8 |
| 66= | University of Miyazaki | 8.8 |
| 66= | Showa University | 8.8 |
| 70= | Jikei University School of Medicine | 8.6 |
| 70= | Kanagawa University | 8.6 |
| 72 | Shibaura Institute of Technology Tokyo | 8.5 |
| 73 | Tokai University | 8.3 |
| 74= | Chiba Institute of Technology | 8.2 |
| 74= | Kogakuin University | 8.2 |
| 76= | Meijo University | 8.1 |
| 76= | Tottori University | 8.1 |
| 78 | Hosei University | 8 |
| 79 | Tokyo Denki University | 7.9 |
| 80 | Saitama Medical University | 7.8 |
| 81 | Fujita Health University | 7.7 |
| 82 | Oita University | 7.6 |
| 83 | Kansai University | 7.3 |
| 84 | Kwansei Gakuin University | 7.1 |
| 85 | Kansai Medical University | 7 |
| 86 | Yokohama City University | 6.5 |
| 87 | Doshisha University | 6.4 |
| 88 | Hamamatsu University School of Medicine | 6 |
| 89 | Ibaraki University | 5.4 |