Purpose: This study aimed to describe the prevalence of vitamin D deficiency in Indonesian children and adolescents. Methods: This was a meta-analysis of prevalence using the Hartung-Knapp-Sidik-Jonkman method with a random effects model. A prediction interval was used to estimate true effects. We searched PubMed, MEDLINE, Cochrane Library, Science Direct, Google Scholar, and 3 Indonesian databases (Indonesian Scientific Journal Database, Neliti, and Indonesia One Search). We included cross-sectional or case-control studies that provided data on the prevalence of vitamin D deficiency. We excluded case reports, case series, cohort studies, or studies outside Indonesia. We computed point prevalence by dividing the number of children with hypovitaminosis D by the total number of subjects in that study. This review was registered with PROSPERO (International Prospective Register of Systematic Reviews) (CRD42022329814). Results: Of 1,397 manuscripts identified, 7 were included in this review. A total of 5,870 children were included in this meta-analysis, ranging in age from 6 months to 19 years. The prevalence of hypovitaminosis D in Indonesia was calculated as 33% (95% confidence interval [CI], 9–56) and was higher in females (60% [95% CI, 58–62]) than in males (40% [95% CI, 38–42]). Mean serum vitamin D level was 22.74 ng/mL (95% CI, 16.95–30.51) with a prediction interval of 15.96 ng/mL to 29.52 ng/mL. Conclusion Vitamin D deficiency is a public health emergency in Indonesia. Strategies to detect and treat vitamin D deficiency in Indonesian children and adolescents should be implemented immediately.