A medical antimicrobial composition includes a siloxanyl structure-containing polymer and an ammonium group-containing polymer, which is excellent in transparency, flexibility and mechanical properties, and also excellent in adhesion to a base resin with good mechanical properties, particularly to a silicone resin. The medical antimicrobial composition includes an ammonium group-containing polymer compound dispersed in a siloxanyl structure-containing polymer and a medical device comprising the medical antimicrobial composition.