| # | University | City | World rank | In-country | Citations |
|---|---|---|---|---|---|
| 201 | Niigata University | not ranked | #23 | 3,615,564 | |
| 202 | Waseda University | not ranked | #24 | 3,526,395 | |
| 203 | Nagasaki University | not ranked | #26 | 3,292,569 | |
| 204 | Tokushima University | not ranked | #27 | 3,201,021 | |
| 205 | Shinshu University | not ranked | #29 | 3,108,425 | |
| 206 | Kyoto Prefectural University of Medicine | not ranked | #31 | 2,534,066 | |
| 207 | Gifu University | not ranked | #32 | 2,525,106 | |
| 208 | Nihon University | not ranked | #33 | 2,454,375 | |
| 209 | Tokyo Metropolitan University | not ranked | #34 | 2,385,790 | |
| 210 | Kagoshima University | not ranked | #36 | 2,360,733 | |
| 211 | Jichi Medical School | not ranked | #37 | 2,342,339 | |
| 212 | Kinki University | not ranked | #35 | 2,320,466 | |
| 213 | Tokyo Women's Medial College | not ranked | #40 | 2,140,219 | |
| 214 | Nagoya City University | not ranked | #41 | 2,119,550 | |
| 215 | Yamaguchi University | not ranked | #42 | 2,111,686 | |
| 216 | Mie University | not ranked | #43 | 2,089,402 | |
| 217 | Tokyo University of Agriculture and Technology | not ranked | #45 | 1,971,139 | |
| 218 | Osaka Prefectural University | not ranked | #47 | 1,956,908 | |
| 219 | Sapporo Medical University | not ranked | #46 | 1,930,532 | |
| 220 | Nara Institute of Science and Technology | not ranked | #48 | 1,889,123 | |
| 221 | Showa University | not ranked | #50 | 1,791,199 | |
| 222 | Yamagata University | not ranked | #52 | 1,663,727 | |
| 223 | Graduate University for Advanced Studies | not ranked | #53 | 1,612,624 | |
| 224 | Nippon Medical School | not ranked | #54 | 1,538,603 | |
| 225 | Fukuoka University | not ranked | #57 | 1,499,510 | |
| 226 | Tokyo Medical College | not ranked | #58 | 1,399,661 | |
| 227 | Nara Medical University | not ranked | #60 | 1,392,637 | |
| 228 | Hirosaki University | not ranked | #61 | 1,361,622 | |
| 229 | Shiga University of Medical Science | not ranked | #64 | 1,320,106 | |
| 230 | Yamanashi University | not ranked | #63 | 1,310,943 | |
| 231 | Hyogo College of Medicine | not ranked | #66 | 1,291,932 | |
| 232 | University of Occupational and Environmental Health, Japan | not ranked | #67 | 1,276,362 | |
| 233 | Shimane University | not ranked | #70 | 1,244,901 | |
| 234 | Saitama Medical School | not ranked | #71 | 1,239,430 | |
| 235 | Shizuoka University | not ranked | #74 | 1,202,750 | |
| 236 | Kyoto Pharmaceutical University | not ranked | #75 | 1,177,812 | |
| 237 | Miyazaki University | not ranked | #77 | 1,143,313 | |
| 238 | Wakayama Medical College | not ranked | #78 | 1,130,450 | |
| 239 | Nagoya Institute of Technology | not ranked | #79 | 1,122,754 | |
| 240 | Kyoto University of Education | not ranked | #80 | 1,102,950 | |
| 241 | University of the Ryukyus | not ranked | #81 | 1,079,527 | |
| 242 | National Defence Medical College | not ranked | #83 | 1,015,902 | |
| 243 | Saga University | not ranked | #84 | 1,009,840 | |
| 244 | Ritsumeikan University | not ranked | #86 | 921,093 | |
| 245 | Kyorin University | not ranked | #88 | 896,297 | |
| 246 | Tokyo University of Agriculture | not ranked | #85 | 895,800 | |
| 247 | Iwate Medical University | not ranked | #90 | 880,903 | |
| 248 | Saitama University | not ranked | #91 | 876,345 | |
| 249 | Oita University | not ranked | #92 | 862,873 | |
| 250 | Kyushu Institute of Technology | not ranked | #95 | 816,469 |
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.