| City | Region |
|---|
| ›Sabang | Sumatra› |
| ›Sabulu | Sulawesi› |
| ›Sailolof | Irian Jaya› |
| ›Salamban | South Kalimantan› |
| ›Samarinda | East Kalimantan› |
| ›Sambaliung | East Kalimantan› |
| ›Sambas | West Kalimantan› |
| ›Sambiat | Sulawesi› |
| ›Sambu | Sumatra (Kepulauan Riau)› |
| ›Sampaga | Sulawesi› |
| ›Sampit | Central Kalimantan› |
| ›Sangkulirang | East Kalimantan› |
| ›Saparua | Moluccas (Ceram Island)› |
| ›Sarmi | Irian Jaya› |
| ›Saukris | Irian Jaya› |
| ›Sawahlunto | Sumatra› |
| ›Sawai | Irian Jaya› |
| ›Sawan | Bali› |
| ›Sawan | East Kalimantan› |
| ›Sawu | Nusa Tenggara Timur (Sawu Island)› |
| ›Sedati | Jawa› |
| ›Segeri | Sulawesi› |
| ›Seipinang | Central Kalimantan› |
| ›Sejaka | South Kalimantan› |
| ›Sele | Irian Jaya› |
| ›Selemadeg | Bali› |
| ›Semarang | Jawa› |
| ›Senduro | Jawa› |
| ›Senduruhan | West Kalimantan› |
| ›Serang | Jawa› |
| ›Serikkambelo | Moluccas (Ceram Island)› |
| ›Serui | Irian Jaya› |
| ›Sesepe | Moluccas (Kepulauan Obi)› |
| ›Sewer | Moluccas (Kepulauan Aru)› |
| ›Siau Island | Sulawesi (Kepulauan Sangir)› |
| ›Sibolga | Sumatra› |
| ›Sidoarjo | Jawa› |
| ›Sigli | Sumatra› |
| ›Sijunjung | Sumatra› |
| ›Sikeli | Sulawesi› |
| ›Silo | Jawa› |
| ›Simpang | Sumatra› |
| ›Sinabang | Sumatra (Simeulue Island)› |
| ›Sindangbarang | Jawa› |
| ›Singaraja | Bali› |
| ›Singkang | Sulawesi› |
| ›Singkawang | West Kalimantan› |
| ›Sinjai | Sulawesi› |
| ›Sintang | West Kalimantan› |
| ›Slawi | Jawa› |
| ›Soasiu | Halmahera› |
| ›Soe | Nusa Tenggara› |
| ›Sofifi | Moluccas (Halmahera)› |
| ›Solokuro | Jawa› |
| ›Songa | Halmahera› |
| ›Sopi | Halmahera› |
| ›Sorong | Irian Jaya› |
| ›Sragen | Jawa› |
| ›Subang | Jawa› |
| ›Sukabumi | Jawa› |
| ›Sukadana | West Kalimantan› |
| ›Sukadana | Sumatra› |
| ›Sukanegara | Jawa› |
| ›Sukaramai | Central Kalimantan› |
| ›Sukasada | Bali› |
| ›Sumbawa Besar | Nusa Tenggara› |
| ›Sumber Baru | Jawa› |
| ›Sumbermanjing | Jawa› |
| ›Sumberrejo | Jawa› |
| ›Sumenep | Jawa (Madura Island)› |
| ›Sungai Liat | Sumatra (Bangka Island)› |
| ›Sungai Mandau | Sumatra› |
| ›Sungaidareh | Sumatra› |
| ›Sungaigerong | Sumatra› |
| ›Sungailimau | Sumatra› |
| ›Sungaipenuh | Sumatra› |
| ›Surabaya | Jawa› |
| ›Surakarta | Jawa› |
| ›Surulangun | Sumatra› |
| ›Suwakong | East Kalimantan› |
