Background: Streptococcus pneumoniae may asymptomatically colonize the human nasopharynx and remains a leading cause of invasive and noninvasive disease in children, accounting for an estimated 294,000 global deaths in those aged under five years. Nationally representative serotype data from Indonesia remain limited despite national PCV13 rollout in 2022. This study aims to evaluate the distribution of Streptococcus pneumoniae serotypes and estimate the coverage of pneumococcal conjugate vaccines (PCVs) among children aged 0–18 years in Indonesia. Methods: Systematic search of PubMed, Scopus, ScienceDirect, Google Scholar, and Paediatrica Indonesiana (to December 2025) for observational studies (PROSPERO CRD420251239935). The extracted data included the study period, setting, population, specimen type, serotypes, sample size, and nasopharyngeal carriage. Pooled serotype prevalence is calculated; vaccine coverage estimated for pneumococcal conjugate vaccines containing 10 (PCV10), 13 (PCV13), 15 (PCV15), and 20 (PCV20) serotypes assuming vaccine-type priority in multicolonization. Risk of bias assessed using the Joanna Briggs Institute’s checklist for prevalence studies. Results: Nineteen studies across 13 regions of Indonesia involving children aged 0–18 years included. Nasopharyngeal carriage ranged from 21.0% to 87.6% in healthy children and 9.2% to 73% in children with illnesses. The most common serotypes were 19F, 23F, 6B, 14, 19A, and 34. Non-typeable isolates accounted for more than 20% of all isolates in several studies. The pooled coverage for PCV10, PCV13, PCV15, and PCV20 was 40.3%, 50.2%, 50.8%, and 57.0% respectively. Low-moderate RoB (63% low). Conclusions: The dominant serotypes largely included in PCV13. Active surveillance is required to monitor serotype shifts and ensure the long-term effectiveness of the national vaccination program. © 2026 by the authors.