Background Chronic kidney disease (CKD) is an emerging public health issue globally. The prevalence estimates on CKD in South Asia are however limited. This study aimed to examine the prevalence of CKD among the general and high-risk population in South Asia. Methods We conducted a systematic review and meta-analysis of population-level prevalence studies in South Asia (Afghanistan, Bangladesh, Bhutan, Maldives, Nepal, India, Pakistan, and Sri Lanka). Three databases namely PubMed, Scopus and Web of Science were systematically searched for published reports of kidney disease in South Asia up to 28 October 2020. A random-effect model for computing the pooled prevalence was used. Results Of the 8749 identified studies, a total of 24 studies were included in the review. The pooled prevalence of CKD among the general population was 14% (95% CI 11-18%), and 15% (95% CI 11-20%) among adult males and 13% (95% CI 10-17%) in adult females. The prevalence of CKD was 27% (95% CI 20-35%) in adults with hypertension, 31% (95% CI 22-41%) in adults with diabetes and 14% (95% CI 10-19%) in adults who were overweight/obese. We found substantial heterogeneity across the included studies in the pooled estimates for CKD prevalence in both general and high-risk populations. The prevalence of CKD of unknown origin in the endemic population was 8% (95% CI 3-16%). Conclusion Our study reaffirms the previous reports that CKD represents a serious public health challenge in South Asia, with the disease prevalent among 1 in 7 adults in South Asian countries.