A global increase in severe group A Streptococcus (GAS) infections has been reported following the COVID-19 pandemic, but data from Asia remain limited. We examined epidemiology and clinical characteristics of severe paediatric GAS infections across 86 Japanese hospitals, focusing on patients under 18 years of age, hospitalized between 1 January 2019 and 31 March 2024. Severe GAS infection was defined by the isolation of GAS from sterile sites, or from non-sterile sites under specific conditions, such as streptococcal toxic shock syndrome (STSS). A total of 83 cases were analysed. Cases increased from the summer of 2023, exceeding pre-pandemic levels. The median age was 4 (interquartile range: 1–8) years, with the highest number among 1-year-olds. No cases were reported in Hokkaido, northern Japan. Only 6% (5/83) of the cases had preceding GAS pharyngitis. Pneumonia was the most prevalent diagnosis (25%), with 76% of these cases being complicated by empyema, often necessitating intensive care or surgical intervention. Only 17% (14/83) of cases were reported as STSS in Japan’s national surveillance system. This study represents the first multicentre nationwide hospital-based investigation of severe paediatric GAS infections in Japan, identifying the recent increase in cases, thereby highlighting limitations of current STSS-based surveillance.