| Rank | university | country | city | GLOBAL SCORE | ENROLLMENT |
| #1 in Best Universities in Japan #73 in Best Global Universities |
University of Tokyo | Japan | Tokyo | 72.8 | 25,935 |
| #2 in Best Universities in Japan #125 in Best Global Universities |
Kyoto University | Japan | Kyoto | 67.9 | N/A |
| #3 in Best Universities in Japan #252 in Best Global Universities |
Osaka University | Japan | Suita | 60.0 | 22,867 |
| #4 in Best Universities in Japan #269 in Best Global Universities |
Tohoku University | Japan | Sendai | 59.4 | 17,752 |
| #5 in Best Universities in Japan #310 in Best Global Universities |
Nagoya University | Japan | Nagoya | 57.6 | 15,589 |
| #6 in Best Universities in Japan #316 in Best Global Universities |
Tokyo Institute of Technology | Japan | Tokyo | 57.4 | 9,566 |
| #7 in Best Universities in Japan #329 in Best Global Universities |
Kyushu University | Japan | Fukuoka | 56.7 | N/A |
| #8 in Best Universities in Japan #395 in Best Global Universities |
University of Tsukuba | Japan | Tsukuba | 54.1 | 16,633 |
| #9 in Best Universities in Japan #437 in Best Global Universities |
Hokkaido University | Japan | Sapporo | 52.8 | 18,483 |
| #10 in Best Universities in Japan #467 in Best Global Universities |
Waseda University | Japan | Tokyo | 51.4 | 48,260 |
| #11 in Best Universities in Japan #529 in Best Global Universities |
Kobe University | Japan | Kobe | 49.4 | 15,676 |
| #12 in Best Universities in Japan #538 in Best Global Universities |
Keio University | Japan | Tokyo | 49.1 | 34,498 |
| #13 in Best Universities in Japan #580 in Best Global Universities |
Tokyo Metropolitan University | Japan | Tokyo | 48.2 | N/A |
| #14 in Best Universities in Japan #639 in Best Global Universities |
Hiroshima University | Japan | Hiroshima | 46.4 | 15,080 |
| #14 in Best Universities in Japan #639 in Best Global Universities |
Okayama University | Japan | Okayama City | 46.4 | 13,136 |
| #16 in Best Universities in Japan #774 in Best Global Universities |
Shinshu University | Japan | Matsumoto | 42.2 | N/A |
| #17 in Best Universities in Japan #779 in Best Global Universities |
Tokyo Medical and Dental University | Japan | Tokyo | 42.1 | N/A |
| #18 in Best Universities in Japan #792 in Best Global Universities |
Chiba University | Japan | Chiba-shi | 41.5 | 13,764 |
| #19 in Best Universities in Japan #864 in Best Global Universities |
Graduate University for Advanced Studies - Japan | Japan | Hayama | 40.0 | N/A |
| #20 in Best Universities in Japan #904 in Best Global Universities |
Tokyo University of Science | Japan | Tokyo | 38.6 | N/A |
| #21 in Best Universities in Japan #936 in Best Global Universities |
Yokohama City University | Japan | Yokohama | 37.5 | 4,976 |
| #22 in Best Universities in Japan #965 in Best Global Universities |
Niigata University | Japan | Niigata | 36.9 | N/A |
| #23 in Best Universities in Japan #984 in Best Global Universities |
University of Occupational & Environmental Health - Japan | Japan | Fukuoka | 36.3 | N/A |
| #24 in Best Universities in Japan #990 in Best Global Universities |
Kanazawa University | Japan | Kanazawa | 36.1 | 10,341 |
| #25 in Best Universities in Japan #1,016 in Best Global Universities |
Kumamoto University | Japan | Kumamoto | 35.4 | 10,045 |
| #26 in Best Universities in Japan #1,022 in Best Global Universities |
Ritsumeikan University | Japan | Kyoto | 35.2 | N/A |
| #27 in Best Universities in Japan #1,031 in Best Global Universities |
Nagasaki University | Japan | Nagasaki | 35.0 | N/A |
| #28 in Best Universities in Japan #1,044 in Best Global Universities |
Teikyo University | Japan | Tokyo | 34.7 | N/A |
| #29 in Best Universities in Japan #1,106 in Best Global Universities |
Tokai University | Japan | Hiratsuka | 33.2 | 29,644 |
| #30 in Best Universities in Japan #1,117 in Best Global Universities |
Tokyo University of Agriculture | Japan | Tokyo | 32.9 | N/A |
| #31 in Best Universities in Japan #1,125 in Best Global Universities |
Osaka City University | Japan | Osaka | 32.7 | 8,019 |
| #32 in Best Universities in Japan #1,134 in Best Global Universities |
Nara Institute of Science | Japan | Ikoma | 32.5 | N/A |
| #33 in Best Universities in Japan #1,148 in Best Global Universities |
Fujita Health University | Japan | Toyoake | 32.2 | 3,490 |
| #34 in Best Universities in Japan #1,163 in Best Global Universities |
Kinki University (Kindai University) | Japan | Higashiosaka | 31.8 | 33,614 |
| #35 in Best Universities in Japan #1,174 in Best Global Universities |
Kagoshima University | Japan | Kagoshima | 31.5 | N/A |
| #36 in Best Universities in Japan #1,187 in Best Global Universities |
Tokyo Medical University | Japan | Tokyo | 31.3 | N/A |
| #37 in Best Universities in Japan #1,215 in Best Global Universities |
Nihon University | Japan | Tokyo | 30.6 | N/A |
| #38 in Best Universities in Japan #1,234 in Best Global Universities |
Juntendo University | Japan | Tokyo | 30.1 | 4,953 |
| #38 in Best Universities in Japan #1,234 in Best Global Universities |
Tokushima University | Japan | Tokushima | 30.1 | N/A |
| #40 in Best Universities in Japan #1,238 in Best Global Universities |
Ehime University | Japan | Matsuyama | 30.0 | N/A |
| #41 in Best Universities in Japan #1,266 in Best Global Universities |
Kyushu Institute of Technology | Japan | Fukuoka | 29.4 | 5,649 |
| #42 in Best Universities in Japan #1,271 in Best Global Universities |
Okinawa Institute of Science and Technology Graduate University | Japan | Kunigami | 29.3 | N/A |
| #43 in Best Universities in Japan #1,281 in Best Global Universities |
University of Toyama | Japan | Toyama | 29.2 | N/A |
| #44 in Best Universities in Japan #1,315 in Best Global Universities |
Yamaguchi University | Japan | Yamaguchi City | 28.3 | N/A |
| #45 in Best Universities in Japan #1,321 in Best Global Universities |
University of Electro-Communications - Japan | Japan | Tokyo | 28.2 | 4,838 |
| #46 in Best Universities in Japan #1,333 in Best Global Universities |
Gifu University | Japan | Gifu | 28.0 | 7,405 |
| #47 in Best Universities in Japan #1,335 in Best Global Universities |
Yokohama National University | Japan | Yokohama | 27.9 | 10,120 |
| #48 in Best Universities in Japan #1,348 in Best Global Universities |
Shizuoka University | Japan | Suruga-ku, Shizuoka City | 27.5 | N/A |
| #49 in Best Universities in Japan #1,352 in Best Global Universities |
Toho University | Japan | Tokyo | 27.3 | N/A |
| #50 in Best Universities in Japan #1,360 in Best Global Universities |
Jikei University | Japan | Tokyo | 27.1 | N/A |
| #51 in Best Universities in Japan #1,381 in Best Global Universities |
Gunma University | Japan | Maebashi | 26.4 | N/A |
| #51 in Best Universities in Japan #1,381 in Best Global Universities |
Tokyo Women's Medical University | Japan | Tokyo | 26.4 | N/A |
| #53 in Best Universities in Japan #1,390 in Best Global Universities |
Kochi University | Japan | Kochi | 26.2 | N/A |
| #53 in Best Universities in Japan #1,390 in Best Global Universities |
Yamagata University | Japan | Yamagata | 26.2 | 8,905 |
| #55 in Best Universities in Japan #1,405 in Best Global Universities |
Nagoya Institute of Technology | Japan | Nagoya | 26.0 | N/A |
| #56 in Best Universities in Japan #1,409 in Best Global Universities |
University of Yamanashi | Japan | Kofu | 25.9 | N/A |
| #57 in Best Universities in Japan #1,413 in Best Global Universities |
Japan Advanced Institute of Science & Technology (JAIST) | Japan | Nomi | 25.7 | N/A |
| #57 in Best Universities in Japan #1,413 in Best Global Universities |
Mie University | Japan | Tsu | 25.7 | N/A |
| #59 in Best Universities in Japan #1,423 in Best Global Universities |
Osaka Prefecture University | Japan | Sakai | 25.4 | 7,710 |
| #60 in Best Universities in Japan #1,429 in Best Global Universities |
Saitama University | Japan | Saitama City | 25.3 | N/A |
| #61 in Best Universities in Japan #1,432 in Best Global Universities |
Kagawa University | Japan | Takamatsu | 25.2 | N/A |
| #62 in Best Universities in Japan #1,452 in Best Global Universities |
University of Ryukyus | Japan | Nishihara | 24.5 | N/A |
| #63 in Best Universities in Japan #1,459 in Best Global Universities |
Kitasato University | Japan | Tokyo | 24.3 | N/A |
| #64 in Best Universities in Japan #1,496 in Best Global Universities |
Jichi Medical University | Japan | Shimotsuke | 22.9 | N/A |
| #64 in Best Universities in Japan #1,496 in Best Global Universities |
Kyoto Institute of Technology | Japan | Kyoto | 22.9 | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Fukuoka University | Japan | Fukuoka | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Hamamatsu University School of Medicine | Japan | Hamamatsu | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Hiroshima Institute of Technology | Japan | Hiroshima | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Hyogo College of Medicine | Japan | Nishinomiya | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Iwate University | Japan | Morioka | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Kanazawa Medical University | Japan | Kahoku | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Kawasaki Medical School | Japan | Kurashiki | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Kurume University | Japan | Kurume | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Kyoto Prefectural University of Medicine | Japan | Kyoto | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Kyoto University of Education | Japan | Kyoto | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Nagasaki Institute of Applied Science | Japan | Nagasaki | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Nara Medical University | Japan | Kashihara | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Nippon Medical School | Japan | Tokyo | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Ochanomizu University | Japan | Tokyo | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Osaka Medical College | Japan | Osaka | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Rikkyo University | Japan | Tokyo | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Saitama Medical University | Japan | Iruma | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Shiga University of Medical Science | Japan | Otsu | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Showa University | Japan | Tokyo | N/A | N/A |
| #Unranked in Best Universities in Japan #Unranked in Best Global Universities |
Wakayama Medical University | Japan | Wakayama | N/A | N/A |
