Background: Primary peritonitis due to Streptococcus pyogenes (S. pyogenes) is uncommon in patients without comorbid conditions such as immunosuppression, nephritic disease, or liver cirrhosis. Furthermore, it does not cause another infection at the same time in a healthy person. However, several S. pyogenes mutants have been reported, and some of them exhibit strong virulence. Mutation of the control of virulence (cov) S gene of Streptococcus enhances bacterium survival by repressing negative regulators of virulence, which causes bacterial invasion of aseptic tissues, such as the parenteral space. We report a case of primary peritonitis and subsequent necrotizing fasciitis by the same S. pyogenes species with mutated covS in a previously healthy woman. Case presentation: We present the case of a 55-year-old woman admitted to the hospital due to abdominal pain and nausea. She was treated for peritonitis. A few days later, she became hypotensive and tachycardic and was transferred to the intensive care unit (ICU) for the treatment of septic shock with primary peritonitis. On the second day of her ICU stay, both of her forearms developed swelling and redness around the peripheral injection site. The patient had developed necrotizing fasciitis. Since her skin symptoms spread rapidly, urgent debridement was performed. Her condition improved with antibiotic treatment and multiple episodes of debridement. S. pyogenes was detected in cultures of the patient's blood, ascites, and skin. The identified strain was emm89 genotype and had a genetic mutation of covS. Conclusions: S. pyogenes with covS mutation may spread from a portal, such as the upper respiratory tract or digestive system, to all organs immediately, causing septic shock. Infection with S. pyogenes with mutated genes should be considered in the differential diagnosis of gastrointestinal symptoms, even in a previously healthy patient.