| City | Province | Region | 2020 census
| 2010 census
| Change 2010 to 2020 | mid 2024 official estimate | Notes |
| Jakarta | Special Capital Region of Jakarta | Java | | 10,684,946 | | - | - |
| Surabaya | East Java | Java | | 2,921,996 | | - | - |
| Bekasi | West Java | Java | | 2,644,058 | Satellite city of Jakarta | - | - |
| Bandung | West Java | Java | | 2,528,160 | | - | - |
| Medan | North Sumatra | Sumatra | | 2,494,512 | Most populated city outside of Java | - | - |
| Depok | West Java | Java | | 2,163,635 | Satellite city of Jakarta | - | - |
| Tangerang | Banten | Java | | 1,963,970 | Satellite city of Jakarta | - | - |
| Palembang | South Sumatra | Sumatra | | 1,718,440 | | - | - |
| Semarang | Central Java | Java | | 1,702,379 | | - | - |
| Makassar | South Sulawesi | Sulawesi | | 1,474,393 | Most populated city of Eastern Indonesia | - | - |
| South Tangerang | Banten | Java | | 1,399,500 | Satellite city of Jakarta | - | - |
| Batam | Riau Islands | Sumatra | | 1,256,610 | | - | - |
| Bogor | West Java | Java | | 1,078,351 | Satellite city of Jakarta | - | - |
| Pekanbaru | Riau | Sumatra | | 1,123,348 | | - | - |
| Bandar Lampung | Lampung | Sumatra | | 1,214,330 | | - | - |
| Padang | West Sumatra | Sumatra | | 942,938 | | - | - |
| Samarinda | East Kalimantan | Kalimantan | | 861,878 | | - | - |
| Malang | East Java | Java | | 872,694 | | - | - |
| Tasikmalaya | West Java | Java | | 750,730 | | - | - |
| Serang | Banten | Java | | 734,870 | | - | - |
| Balikpapan | East Kalimantan | Kalimantan | | 738,532 | | - | - |
| Banjarmasin | South Kalimantan | Kalimantan | | 675,915 | | - | - |
| Pontianak | West Kalimantan | Kalimantan | | 675,468 | | - | - |
| Denpasar | Bali | Lesser Sunda Islands | | 660,984 | | - | - |
| Jambi | Jambi | Sumatra | | 627,774 | | - | - |
| Cimahi | West Java | Java | | 598,700 | Satellite city of Bandung | - | - |
| Surakarta | Central Java | Java | | 589,242 | | - | - |
| Kupang | East Nusa Tenggara | Lesser Sunda Islands | | 466,632 | | - | - |
| Manado | North Sulawesi | Sulawesi | | 458,582 | | - | - |
| Cilegon | Banten | Java | | 455,620 | | - | - |
| Mataram | West Nusa Tenggara | Lesser Sunda Islands | | 441,147 | | - | - |
| Jayapura | Papua | Western New Guinea | | 414,862 | | - | - |
| Bengkulu | Bengkulu | Sumatra | | 391,117 | | - | - |
| Palu | Central Sulawesi | Sulawesi | | 387,493 | | - | - |
| Yogyakarta | Special Region of Yogyakarta | Java | | 375,780 | | - | - |
| Sukabumi | West Java | Java | | 365,740 | | - | - |
| Ambon | Maluku | Maluku Islands | | 354,052 | | - | - |
| Kendari | Southeast Sulawesi | Sulawesi | | 351,085 | | - | - |
| Cirebon | West Java | Java | | 344,851 | | - | - |
| Dumai | Riau | Sumatra | | 338,064 | | - | - |
| Pekalongan | Central Java | Java | | 318,221 | | - | - |
| Palangka Raya | Central Kalimantan | Kalimantan | | 305,797 | | - | - |
| Binjai | North Sumatra | Sumatra | | 303,272 | Satellite city of Medan | - | - |
| Kediri | East Java | Java | | 298,227 | | - | - |
| Sorong | Southwest Papua | Western New Guinea | | 294,978 | | - | - |
| Pematangsiantar | North Sumatra | Sumatra | | 274,838 | | - | - |
| Banjarbaru | South Kalimantan | Kalimantan | | 272,763 | Satellite city of Banjarmasin | - | - |
| Tegal | Central Java | Java | | 294,477 | | - | - |
| Banda Aceh | Aceh | Sumatra | | 261,969 | | - | - |
| Tarakan | North Kalimantan | Kalimantan | | 249,960 | | - | - |
| Probolinggo | East Java | Java | | 249,539 | | - | - |
| Singkawang | West Kalimantan | Kalimantan | | 246,112 | | - | - |
| Lubuklinggau | South Sumatra | Sumatra | | 246,046 | | - | - |
| Padangsidempuan | North Sumatra | Sumatra | | 236,217 | | - | - |
| Tanjungpinang | Riau Islands | Sumatra | | 234,840 | | - | - |
| Bitung | North Sulawesi | Sulawesi | | 232,440 | Satellite city of Manado | - | - |
| Pangkalpinang | Bangka Belitung Islands | Sumatra | | 226,297 | | - | - |
| Batu | East Java | Java | | 222,685 | | - | - |
| Pasuruan | East Java | Java | | 219,392 | | - | - |
| Banjar | West Java | Java | | 209,790 | | - | - |
| Gorontalo | Gorontalo | Sulawesi | | 205,390 | | - | - |
| Ternate | North Maluku | Maluku Islands | | 204,920 | | - | - |
| Madiun | East Java | Java | | 201,767 | | - | - |
| Salatiga | Central Java | Java | | 198,971 | Satellite city of Semarang | - | - |
| Prabumulih | South Sumatra | Sumatra | | 203,312 | | - | - |
| Lhokseumawe | Aceh | Sumatra | | 196,067 | | - | - |
| Langsa | Aceh | Sumatra | | 194,730 | | - | - |
| Bontang | East Kalimantan | Kalimantan | | 189,968 | | - | - |
| Tanjungbalai | North Sumatra | Sumatra | | 183,170 | | - | - |
| Tebing Tinggi | North Sumatra | Sumatra | | 178,914 | | - | - |
| Metro | Lampung | Sumatra | | 175,710 | | - | - |
| Palopo | South Sulawesi | Sulawesi | | 177,526 | | - | - |
| Bima | West Nusa Tenggara | Lesser Sunda Islands | | 161,362 | | - | - |
| Baubau | Southeast Sulawesi | Sulawesi | | 161,280 | | - | - |
| Parepare | South Sulawesi | Sulawesi | | 160,309 | | - | - |
| Blitar | East Java | Java | | 154,867 | | - | - |
| Pagar Alam | South Sumatra | Sumatra | | 149,199 | | - | - |
| Nusantara | Nusantara Capital City | Kalimantan | | 147,430 | | - | - |
| Payakumbuh | West Sumatra | Sumatra | | 144,830 | | - | - |
| Gunungsitoli | North Sumatra | Sumatra | | 142,890 | | - | - |
| Mojokerto | East Java | Java | | 137,393 | Satellite city of Surabaya | - | - |
| Bukittinggi | West Sumatra | Sumatra | | 124,047 | | - | - |
| Kotamobagu | North Sulawesi | Sulawesi | | 123,918 | | - | - |
| Magelang | Central Java | Java | | 128,709 | | - | - |
| Tidore Islands | North Maluku | Maluku Islands | | 118,613 | | - | - |
| Tomohon | North Sulawesi | Sulawesi | | 103,072 | Satellite city of Manado | - | - |
| Sungai Penuh | Jambi | Sumatra | | 99,771 | | - | - |
| Subulussalam | Aceh | Sumatra | | 97,770 | | - | - |
| Pariaman | West Sumatra | Sumatra | | 97,206 | | - | - |
| Sibolga | North Sumatra | Sumatra | | 91,265 | | - | - |
| Tual | Maluku | Maluku Islands | | 90,007 | | - | - |
| Solok | West Sumatra | Sumatra | | 77,842 | | - | - |
| Sawahlunto | West Sumatra | Sumatra | | 67,760 | | - | - |
| Padang Panjang | West Sumatra | Sumatra | | 58,627 | | - | - |
| Sabang | Aceh | Sumatra | | 43,527 | | - | - |