S
- Sæl (Norway): 107-ton 1. class torpedo boat
- Sælen (Denmark): 108-ton torpedo boat
- Safari (UK): 217-foot submarine S3 class submarine
- Salta (Argentina): 920-ton submarine
- Santa Fe (Argentina): 920-ton submarine
- Santa Marta (Colombia): 142-ton gunboat
- Santiago del Estero (Argentina): 920-ton submarine
- Saranda (Albania): 46-ton patrol boat
- Saukko (Finland): 142-ton submarine
- Seraph (UK): 217-foot submarine S3 class submarine
- Shu Shen (China): 380-ton gunboat
- Siofuk (Austria): 50-ton patrol boat, became the Birago (Germany)
- Sixtus (Denmark): 186-ton minelayer
- Sleipner (Norway): 735-ton Sleipner class destroyer
- Smely (Bulgaria): 97-ton torpedo boat and minesweeper
- Smok (Poland) 711-ton Tugboat
- Søhunden (Denmark): 108-ton torpedo boat and minesweeper
- Sokół (Poland): 540-ton Ursula class submarine
- Søridderen (Denmark): 108-ton torpedo boat and minesweeper, became Hajen (Germany)
- Spiteful (UK): 217-foot submarine S3 class submarine
- Springeren (Denmark): 108-ton torpedo boat and minesweeper
- Stegg (Norway): 256-ton Trygg class torpedo boat
- Støren (Denmark): 108-ton torpedo boat and minesweeper
- Storm (Norway): 107-ton torpedo boat
- Strogi (Bulgaria): 97-ton torpedo boat and minesweeper
- Sulev (Estonia): 228-ton torpedo boat, became Ametist (USSR)
- Suurop (Estonia): 500-ton sidewheeler minelayer and minesweeper
Read more about this topic: List Of World War II Ships Of Less Than 1000 Tons