| 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. Score (FTE) | Ref. World Rank (FTE) |
| 12 | The University of Tokyo | 1 | 74.39 | 62.51 | 34.41 | 31.61 | 28.98 | 54.93 | 24.83 | 27.45 | 42.02 | 35.56 | 27 |
| 28 | Kyoto University | 2 | 54.27 | 46.92 | 24.07 | 21.51 | 27.79 | 46.48 | 14.75 | 21.93 | 32.25 | 34.81 | 31 |
| 38 | Osaka University | 3 | 46.84 | 37.46 | 21.35 | 18.40 | 28.57 | 42.25 | 12.81 | 14.58 | 27.82 | 31.26 | 52 |
| 51 | Tohoku University | 4 | 44.03 | 38.64 | 15.16 | 15.95 | 21.58 | 40.85 | 9.88 | 12.93 | 25.13 | 26.26 | 76 |
| 117 | Nagoya University | 5 | 29.51 | 24.82 | 11.19 | 10.24 | 23.76 | 32.39 | 6.75 | 9.10 | 18.81 | 23.90 | 98 |
| 127 | Kyushu University | 6 | 30.49 | 25.88 | 10.11 | 9.38 | 20.77 | 30.99 | 5.20 | 10.14 | 18.16 | 21.56 | 137 |
| 147 | Tokyo Institute of Technology | 7 | 26.03 | 20.49 | 8.44 | 7.87 | 20.33 | 32.39 | 5.99 | 8.66 | 16.99 | 29.24 | 60 |
| 158 | Hokkaido University | 8 | 29.35 | 24.71 | 9.03 | 8.85 | 19.28 | 28.17 | 3.52 | 8.58 | 16.57 | 18.83 | 191 |
| 194 | University of Tsukuba | 9 | 18.83 | 15.70 | 6.49 | 6.38 | 21.58 | 32.39 | 4.20 | 6.08 | 14.92 | 19.56 | 180 |
| 239 | Hiroshima University | 10 | 11.36 | 11.50 | 4.65 | 5.60 | 25.64 | 29.58 | 3.23 | 5.92 | 13.16 | 17.66 | 220 |
| 263 | Keio University | 11 | 13.21 | 11.70 | 4.81 | 4.44 | 22.81 | 28.17 | 1.99 | 4.92 | 12.37 | 11.36 | 410 |
| 295 | Kobe University | 12 | 11.50 | 11.67 | 4.53 | 4.24 | 24.68 | 23.94 | 2.84 | 4.68 | 11.58 | 14.91 | 301 |
| 301 | Chiba University | 13 | 12.88 | 10.17 | 4.79 | 3.90 | 23.30 | 25.35 | 2.38 | 3.24 | 11.42 | 16.17 | 259 |
| 304 | Okayama University | 14 | 13.93 | 11.98 | 4.08 | 4.18 | 18.33 | 26.76 | 1.70 | 3.27 | 11.35 | 15.98 | 263 |
| 326 | Tokyo Medical and Dental University | 15 | 8.03 | 7.06 | 3.74 | 2.98 | 29.19 | 23.94 | 1.31 | 3.03 | 10.54 | 15.71 | 271 |
| 341 | Juntendo University | 16 | 4.42 | 4.29 | 2.35 | 2.42 | 33.30 | 25.35 | 1.18 | 1.46 | 10.14 | 13.34 | 354 |
| 360 | Kanazawa University | 17 | 9.64 | 8.40 | 3.59 | 3.32 | 23.32 | 21.13 | 1.25 | 2.68 | 9.64 | 15.38 | 290 |
| 363 | Osaka City University | 18 | 8.97 | 6.90 | 3.16 | 2.75 | 22.10 | 22.54 | 1.70 | 2.21 | 9.48 | 14.64 | 311 |
| 383 | Niigata University | 19 | 9.42 | 7.33 | 3.53 | 2.58 | 23.46 | 19.72 | 1.57 | 1.83 | 9.09 | 14.50 | 319 |
| 385 | Tōkai University | 20 | 6.54 | 7.61 | 1.98 | 3.16 | 18.95 | 22.54 | 1.38 | 3.10 | 9.00 | - | - |
| 392 | Kumamoto University | 21 | 8.30 | 6.39 | 3.63 | 2.09 | 27.39 | 18.31 | 1.18 | 2.10 | 8.93 | 13.62 | 349 |
| 398 | Waseda University | 22 | 8.01 | 8.24 | 2.06 | 2.86 | 16.14 | 22.54 | 1.62 | 2.26 | 8.82 | - | - |
| 412 | Tokyo Metropolitan University | 23 | 6.13 | 5.31 | 2.43 | 1.71 | 24.86 | 19.72 | 1.99 | 1.48 | 8.51 | 12.20 | 379 |
| 421 | Yokohama City University | 24 | 4.77 | 4.08 | 2.12 | 1.90 | 27.87 | 19.72 | 0.72 | 1.43 | 8.34 | 11.39 | 408 |
| 428 | Tokyo University of Science | 25 | 8.41 | 6.76 | 2.55 | 2.10 | 18.97 | 19.72 | 1.46 | 1.56 | 8.27 | 12.97 | 361 |
| 437 | The University of Tokushima | 26 | 7.57 | 5.52 | 2.46 | 2.06 | 20.36 | 19.72 | 0.63 | 2.01 | 8.14 | 12.31 | 376 |
| 462 | Nagasaki University | 27 | 7.61 | 6.10 | 2.41 | 2.03 | 19.84 | 18.31 | 0.77 | 1.78 | 7.84 | 10.75 | 439 |
| 470 | Gifu University | 28 | 7.51 | 6.08 | 2.31 | 1.90 | 19.29 | 18.31 | 0.72 | 1.52 | 7.71 | 11.93 | 389 |
| 478 | Tokyo University of Agriculture and Technology | 29 | 6.31 | 5.69 | 1.72 | 1.63 | 17.08 | 19.72 | 1.14 | 1.72 | 7.62 | 11.26 | 414 |
| 479 | Shinshu University | 30 | 7.81 | 6.01 | 2.44 | 2.09 | 19.57 | 16.90 | 0.98 | 1.92 | 7.61 | 11.16 | 419 |
| 482 | Showa University | 31 | 7.55 | 7.67 | 1.56 | 1.86 | 12.97 | 18.31 | 1.03 | 3.99 | 7.58 | 10.20 | 462 |
| 484 | Nagoya City University | 32 | 4.59 | 4.66 | 1.51 | 1.73 | 20.60 | 19.72 | 0.81 | 1.30 | 7.57 | 10.40 | 455 |
| 488 | Ehime University | 33 | 5.65 | 5.17 | 1.84 | 1.68 | 20.40 | 18.31 | 0.87 | 1.84 | 7.54 | 10.94 | 428 |
| 490 | Toyama University | 34 | 6.66 | 5.20 | 1.79 | 2.24 | 16.81 | 19.72 | 0.37 | 1.44 | 7.49 | 11.25 | 415 |
| 490 | Tokyo Women's Medical University | 34 | 4.48 | 3.58 | 1.71 | 1.44 | 23.93 | 18.31 | 0.63 | 1.44 | 7.49 | 10.14 | 465 |