S
- (Bohol) Sondol
- (Province of Cebu) Somosa
- (Province of Cebu) Somimbang
- (Province of Cebu) Solsogan
- (Province of Negros Oriental) Solongon
- (Province of Cebu) Sojoton
- (Province of Negros Oriental) Sitio Nuevo
- (Province of Cebu) Sirao
- (Province of Cebu) Sirao
- (Province of Siquijor) Siquijor Island
- (Province of Cebu) Siotes
- (Province of Cebu) Singsing
- (Bohol) Sinayao
- (Province of Negros Oriental) Sinauran
- (Province of Negros Oriental) Similawa
- (Bohol) Simang
- (Province of Siquijor) Simacolong
- (Province of Cebu) Sima
- (Bohol) Silo Island
- (Bohol) Silob
- (Bohol) Siling
- (Province of Cebu) Sili
- (Province of Cebu) Sili
- (Province of Cebu) Silagon Island
- (Bohol) Sierra Bullones
- (Province of Cebu) Sibonga
- (Province of Cebu) Sibago
- (Province of Cebu) Sibacan
- (Province of Negros Oriental) Siapo
- (Province of Cebu) Secanto