Intestinal protozoan parasites among Asian schoolchildren are a subject of concern due to their prevalence and potential health impact. Understanding and addressing this issue is crucial for public health in the region. We conducted a comprehensive search for articles published up to December 2023 across four databases, including Scopus, PubMed, ProQuest, and Web of Science. To estimate the combined prevalence, a random-effects model with a 95% confidence interval (CI) was applied, and the statistical analysis was performed using meta-analysis packages in R version (3.6.1). This study is registered with PROSPERO (CRD42023481146). Among 131 eligible articles, the prevalence of intestinal protozoan parasites was 0.208 (95% CI = 0.180-0.238). Lebanon and Tajikistan had the highest country-level prevalence at 0.851 and 0.836, respectively, with Giardia duodenalis being the most prevalent species at 0.082. In summary, our study highlights the urgent public health issue of protozoan parasites among Asian schoolchildren due to poor sanitation and water quality. Immediate interventions are essential, considering climate and socioeconomic factors, to combat these infections and improve overall health.