| World Rank▲ | University | Country Rank | 11 years articles | Current articles | 11 years citations | Current citations | Ave. citations | H-Index | HiCi papers | Hi-Impact journal articles | Total score | Ref. World Rank (FTE) |
| 16 | The University of Tokyo | 1 | 68.93 | 57.40 | 34.60 | 34.46 | 31.51 | 56.96 | 23.38 | 26.03 | 41.49 | 12 |
| 33 | Kyoto University | 2 | 50.61 | 40.67 | 24.26 | 23.57 | 30.08 | 45.57 | 14.14 | 17.90 | 30.84 | 42 |
| 52 | Osaka University | 3 | 42.70 | 33.77 | 20.70 | 17.69 | 30.44 | 41.77 | 11.47 | 15.00 | 26.85 | 89 |
| 88 | Tohoku University | 4 | 40.61 | 32.80 | 15.71 | 14.24 | 24.28 | 34.18 | 8.81 | 12.84 | 22.85 | 103 |
| 143 | Nagoya University | 5 | 26.75 | 21.07 | 11.22 | 10.97 | 26.33 | 34.18 | 5.83 | 8.43 | 18.61 | 86 |
| 169 | Tokyo Institute of Technology | 6 | 23.60 | 17.77 | 8.49 | 9.60 | 22.58 | 35.44 | 5.66 | 6.57 | 17.13 | 66 |
| 183 | Hokkaido University | 7 | 27.64 | 21.90 | 9.49 | 8.65 | 21.56 | 29.11 | 3.14 | 8.66 | 16.52 | 172 |
| 186 | Kyushu University | 8 | 28.12 | 22.83 | 10.46 | 8.35 | 23.35 | 25.32 | 4.73 | 8.08 | 16.30 | 184 |
| 239 | University of Tsukuba | 9 | 17.20 | 14.13 | 6.62 | 6.59 | 24.16 | 30.38 | 3.66 | 5.36 | 14.30 | 272 |
| 255 | Hiroshima University | 10 | 15.54 | 11.88 | 5.23 | 6.04 | 21.12 | 34.18 | 2.48 | 3.51 | 13.72 | 255 |
| 284 | Keio University | 11 | 13.48 | 11.58 | 5.40 | 5.58 | 25.16 | 29.11 | 2.29 | 4.82 | 13.01 | 411 |
| 342 | Kobe University | 12 | 11.47 | 9.62 | 4.17 | 4.27 | 22.81 | 25.32 | 2.03 | 3.07 | 11.06 | 367 |
| 345 | Okayama University | 13 | 13.03 | 10.37 | 4.42 | 4.60 | 21.30 | 24.05 | 1.96 | 3.56 | 11.01 | 347 |
| 351 | Tokyo Medical and Dental University | 14 | 7.67 | 6.56 | 3.79 | 3.41 | 31.06 | 25.32 | 1.30 | 2.89 | 10.94 | 292 |
| 353 | Chiba University | 15 | 12.09 | 9.26 | 4.91 | 3.60 | 25.50 | 22.78 | 2.17 | 2.88 | 10.85 | 344 |
| 363 | National Institute of Genetics | 16 | 1.18 | 1.11 | 1.27 | 0.81 | 67.44 | 15.19 | 0.74 | 0.80 | 10.45 | 422 |
| 374 | Waseda University | 17 | 7.99 | 8.02 | 2.40 | 4.05 | 18.82 | 27.85 | 1.55 | 2.24 | 10.27 | - |
| 376 | National Institute for Basic Biology | 18 | 1.16 | 0.87 | 1.25 | 0.74 | 67.72 | 13.92 | 0.87 | 0.71 | 10.20 | 434 |
| 403 | Kanazawa University | 19 | 9.03 | 7.27 | 3.60 | 3.28 | 24.99 | 22.78 | 1.14 | 2.20 | 9.87 | 319 |
| 445 | Osaka City University | 20 | 7.96 | 6.01 | 3.20 | 2.62 | 25.25 | 21.52 | 1.45 | 1.58 | 9.26 | 365 |
| 448 | Juntendo University | 21 | 4.61 | 4.85 | 2.45 | 2.22 | 33.35 | 20.25 | 1.32 | 1.57 | 9.23 | 442 |
| 458 | Kumamoto University | 22 | 7.56 | 6.36 | 3.38 | 2.36 | 28.03 | 18.99 | 1.08 | 2.07 | 9.04 | 381 |
| 473 | The Graduate University for Advanced Studies | 23 | 3.24 | 3.00 | 1.79 | 1.86 | 34.73 | 20.25 | 0.89 | 1.39 | 8.85 | 477 |
| 496 | Yokohama City University | 24 | 4.53 | 4.10 | 2.12 | 2.13 | 29.45 | 20.25 | 0.87 | 1.35 | 8.62 | 444 |