Purpose As certain vaccine serotypes are still circulating within the community during the PCV13 era, we aimed to delineate the clinical features and assess the immunity following breakthrough infections in children. Methods 101 PCVs-vaccinated children < 18 years with culture confirmed PCV13 serotype breakthrough infection (25/101, invasive pneumococcal disease [IPD]) was identified in Taiwan in 2015-2019. Immunoglobulin G (IgG) antibody levels, IgM+ memory B cells (MBCs), and isotype-switched immunoglobulin (sIg+) MBC specific to serotypes 3, 14, 19 A were assessed prior to and one month after an additional PCV13 booster in 9 patients. A cohort of 89 previously vaccinated, healthy children were enrolled as controls. Results The majority (88%) of the breakthrough infection occurred in children under 7 years old. Infection by serotypes 3 and 19 A increased in children aged 5-17 years in 2018-2019. The pre-booster serotype 3- and 19 A-specific IgG in both children with breakthrough infection and controls were lower than the IPD protective thresholds (2.83