| # | University | City | World rank | In-country | Citations |
|---|---|---|---|---|---|
| 1 | University of Tokyo | #36 (2026) | #1 | 47,950,867 | |
| 2 | Kyoto University | Kyoto | #51 (2026) | #2 | 31,703,282 |
| 3 | Institute of Science Tokyo | #84 | #3 | 28,966 | |
| 4 | Tokyo Institute of Technology | #85 (2026) | #4 | 10,021,399 | |
| 5 | Osaka University | Osaka | #91 (2026) | #5 | 26,210,597 |
| 6 | Tohoku University | Sendai | #109 (2026) | #6 | 19,249,279 |
| 7 | Nagoya University | #164 (2026) | #7 | 15,270,331 | |
| 8 | Kyushu University | #170 (2026) | #8 | 14,575,528 | |
| 9 | Hokkaido University | #170 (2026) | #9 | 11,938,279 | |
| 10 | Keio University | #215 (2026) | #10 | 7,593,441 | |
| 11 | Tsukuba University | #350 (2026) | #11 | 9,527,971 | |
| 12 | Toyota Technological Institute | #446 (2024) | #12 | 315,745 | |
| 13 | Hiroshima University | #480 (2026) | #13 | 7,221,262 | |
| 14 | Kobe University | Rokkodai | #482 (2026) | #14 | 7,050,586 |
| 15 | Chiba University | #490 (2023) | #15 | 5,923,170 | |
| 16 | Hitotsubashi University | #539 (2025) | #16 | 159,988 | |
| 17 | Kumamoto University | not ranked | #20 | 4,717,919 | |
| 18 | Juntendo University | not ranked | #25 | 3,360,016 | |
| 19 | Yokohama City University | not ranked | #28 | 3,193,177 | |
| 20 | Gunma University | not ranked | #30 | 2,707,632 | |
| 21 | Ehime University | not ranked | #38 | 2,237,209 | |
| 22 | Kitasato University | not ranked | #39 | 2,189,144 | |
| 23 | Hokkaido Tokai University | not ranked | #44 | 1,997,762 | |
| 24 | Kurume University | not ranked | #49 | 1,807,672 | |
| 25 | Tottori University | not ranked | #51 | 1,679,610 | |
| 26 | Jikei University School of Medicine | not ranked | #55 | 1,520,961 | |
| 27 | Teikyo Heisei University | not ranked | #56 | 1,472,568 | |
| 28 | Toho University | not ranked | #59 | 1,467,760 | |
| 29 | Hamamatsu University School of Medicine | not ranked | #62 | 1,344,652 | |
| 30 | Fujita Health University | not ranked | #65 | 1,313,918 | |
| 31 | Kyoto Bunkyo University | not ranked | #69 | 1,260,409 | |
| 32 | Kagawa University | not ranked | #68 | 1,256,557 | |
| 33 | Fukushima Medical College | not ranked | #72 | 1,237,404 | |
| 34 | Kansai Medical University | not ranked | #73 | 1,228,025 | |
| 35 | Yokohama National University | not ranked | #76 | 1,179,253 | |
| 36 | Akita University | not ranked | #82 | 1,049,755 | |
| 37 | Shizuoka Prefectural University | not ranked | #87 | 896,808 | |
| 38 | University of Electro-Communications | not ranked | #89 | 883,615 | |
| 39 | Kyoto Institute of Technology | not ranked | #93 | 835,107 | |
| 40 | Kochi University | not ranked | #94 | 830,720 | |
| 41 | Tokyo University of Pharmacy and Life Science | not ranked | #103 | 685,607 | |
| 42 | Gifu Pharmaceutical University | not ranked | #110 | 531,996 | |
| 43 | Kwansei Gakuin University | not ranked | #113 | 483,006 | |
| 44 | Hoshi University | not ranked | #115 | 476,535 | |
| 45 | Doshisha University | not ranked | #116 | 473,461 | |
| 46 | Kanagawa University | not ranked | #119 | 430,929 | |
| 47 | University of the Sacred Heart Tokyo | not ranked | #126 | 391,956 | |
| 48 | Utsunomiya University | not ranked | #129 | 376,508 | |
| 49 | Aoyama Gakuin University | Aoyama | not ranked | #130 | 373,119 |
| 50 | Chubu University | not ranked | #133 | 341,404 |
What the two columns mean
In-country is the position the ranking record gives the university among those in its own country, and it is often the more useful number: a university ranked 480th in the world may still be third at home. It is carried over as published, so it does not always follow the order of the other two columns. World rank is the university's QS World University Rankings position. Citations are the number of times work published by the university has been cited, as recorded in OpenAlex; it is the measure used to order universities that QS does not rank at all.
The two do not always agree. A large research university can out-cite a smaller one that sits above it in QS, because QS weighs reputation surveys and staff ratios as well as research.