Streptococcus pyogenes (Group A streptococcus, GAS) is responsible for a various spectrum of diseases, including acute pharyngitis, skin and soft tissue infections (SSTI), invasive diseases and also postinfectious complications, which makes this bacteria a major cause of mortality and morbidity in children throughout the world. The emm typing method is a molecular typing method widely used in classification of GAS and more than 233 types have been reported. Recently a new classification has been developed based on functional and structional properties of M proteins. In this study, isolates collected from 1992 to 2017 among children under 19 years of age in Korea were analyzed by the emm cluster typing system. Among 184 isolates, invasive disease (26, 14.2%), SSTI (46, 25.4%), scarlet fever (50, 27.6%) and acute pharyngitis (60, 32.8%) were included. emm-clusters found among these isolates included A-C3, A-C4, A-C5, E1, E3, E4, E6 and clade Y. A-C4 (20.9%), E1 (20.9%), E4 (20.1%) and A-C3 (19.4%) were the most prevalent and accounted for 81.3% of total isolates. emm-cluster A-C3 and A-C5 were associated with invasive diseases, whereas E1 and A-C4 were associated with non-invasive infections. A-C3 was the most common cluster in invasive diseases by 47.4% and E1 accounted for 48.6% of all scarlet fever cases. There was no predominance for SSTI and pharyngitis, however A-C4 and E4 were the most common clusters in both cases. This study reports epidemiological information of GAS by the new functional classification system among children in Korea.