| # | University | City | World rank | In-country | Citations |
|---|---|---|---|---|---|
| 51 | Universitas Negeri Surabaya | not ranked | #24 | 240,829 | |
| 52 | Universitas Jember | not ranked | #20 | 219,181 | |
| 53 | Universitas Mataram | not ranked | #26 | 208,647 | |
| 54 | Universitas Jambi | not ranked | #27 | 184,791 | |
| 55 | Universitas Lampung | not ranked | #29 | 182,275 | |
| 56 | Universitas Riau | not ranked | #30 | 171,912 | |
| 57 | Universitas Lambung Mangkurat | not ranked | #32 | 155,283 | |
| 58 | Universitas Negeri Makassar | not ranked | #36 | 142,749 | |
| 59 | Universitas Negeri Medan | not ranked | #34 | 137,206 | |
| 60 | Universitas Muhammadiyah Yogyakarta | not ranked | #41 | 119,491 | |
| 61 | Universitas Bengkulu | not ranked | #42 | 118,919 | |
| 62 | Universitas Jenderal Soedirman | not ranked | #40 | 118,532 | |
| 63 | Universitas Tanjungpura | not ranked | #44 | 112,097 | |
| 64 | Universitas Haluoleo | not ranked | #47 | 105,277 | |
| 65 | Universitas Sultan Ageng Tirtayasa | not ranked | #48 | 102,999 | |
| 66 | Universitas Islam Jakarta | not ranked | #50 | 101,848 | |
| 67 | Universitas Muhammadiyah Malang | not ranked | #49 | 101,514 | |
| 68 | Universitas Proklamasi 45 | not ranked | #45 | 95,459 | |
| 69 | Universitas Muhammadiyah Jember | not ranked | #51 | 90,372 | |
| 70 | Universitas Trisakti | not ranked | #52 | 86,945 | |
| 71 | Universitas Tadulako | not ranked | #54 | 82,823 | |
| 72 | Universitas Tarumanagara | not ranked | #55 | 71,396 | |
| 73 | Universitas Muhammadiyah Sumatra Utara | not ranked | #57 | 69,808 | |
| 74 | Universitas Surabaya | not ranked | #53 | 67,866 | |
| 75 | Universitas Islam Bandung | not ranked | #60 | 63,481 | |
| 76 | Universitas Pattimura | not ranked | #61 | 62,526 | |
| 77 | Universitas Dian Nuswantoro | not ranked | #63 | 60,857 | |
| 78 | Universitas Muslim Indonesia | not ranked | #62 | 60,392 | |
| 79 | Universitas Katolik Indonesia Atma Jaya | not ranked | #64 | 59,873 | |
| 80 | Universitas Negeri Gorontalo | not ranked | #65 | 59,261 | |
| 81 | Universitas Trunojoyo Madura | not ranked | #66 | 59,245 | |
| 82 | Universitas Sarjanawiyata Tamansiswa | not ranked | #68 | 56,160 | |
| 83 | Universitas Kristen Petra | not ranked | #67 | 55,664 | |
| 84 | Universitas Nusa Cendana | not ranked | #69 | 54,492 | |
| 85 | Universitas Palangka Raya | not ranked | #70 | 53,662 | |
| 86 | Universitas Pembangunan Nasional "Veteran" Jakarta | not ranked | #71 | 48,382 | |
| 87 | Universitas Islam Sultan Agung | not ranked | #72 | 48,041 | |
| 88 | Universitas Pembangunan Nasional "Veteran" Yogyakarta | not ranked | #73 | 46,573 | |
| 89 | Universitas Muhammadiyah Jakarta | not ranked | #74 | 46,327 | |
| 90 | Universitas Nasional Jakarta | not ranked | #75 | 44,916 | |
| 91 | Universitas Islam Riau | not ranked | #76 | 44,626 | |
| 92 | Universitas Muria Kudus | not ranked | #78 | 44,387 | |
| 93 | Universitas Muhammadiyah Makassar | not ranked | #80 | 42,092 | |
| 94 | Unitomo Surabaya | not ranked | #81 | 41,632 | |
| 95 | Universitas Muhammadiyah Sidoarjo | not ranked | #82 | 40,564 | |
| 96 | Universitas Sanata Dharma | not ranked | #83 | 36,037 | |
| 97 | Universitas Pancasila | not ranked | #85 | 35,933 | |
| 98 | Universitas Katolik Parahyangan | not ranked | #88 | 34,369 | |
| 99 | Universitas Kristen Indonesia | not ranked | #87 | 34,307 | |
| 100 | Universitas Negeri Manado | not ranked | #89 | 33,873 |
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.