S
- (Province of Nueva Vizcaya) Sinal
- (Province of Quirino) Sinadipan
- (Province of Isabela) Sinabbaran
- (Province of Quirino) Sinabbagan
- (Province of Isabela) Simpa
- (Province of Cagayan) Simayung
- (Province of Isabela) Simanu Norte
- (Province of Cagayan) Silong
- (Province of Isabela) Sili
- (Province of Isabela) Silawan
- (Province of Nueva Vizcaya) Silao
- (Province of Cagayan) Siguiran
- (Province of Cagayan) Siguiran
- (Province of Nueva Vizcaya) Siguesu
- (Province of Isabela) Siggud
- (Province of Cagayan) Sidiran
- (Province of Cagayan) Sicalao
- (Province of Isabela) Siffu
- (Province of Cagayan) Sibato Islands
- (Province of Batanes) Stayan Island
- (Province of Nueva Vizcaya) Señora
- (Province of Cagayan) Selong
- (Province of Nueva Vizcaya) Sayuding
- (Province of Batanes) Sanidog
- (Province of Isabela) Saui
- (Province of Isabela) Sarung
- (Province of Cagayan) Sarret
- (Province of Cagayan) Saranay
- (Province of Cagayan) Sarabay
- (Province of Cagayan) San Vicente