Congenital cataract (CC) is the primary cause of treatable childhood blindness worldwide. The establishment of reliable, epidemiological estimates is an essential first step towards management strategies. We undertook an initial systematic review and meta-analysis to estimate the prevalence and other epidemiological characteristics of CC. PubMed, Medline, Web of Science, Embase, and Cochrane Library were searched before January 2015. A meta-analysis with random-effects model based on a proportions approach was performed to determine the population-based prevalence of CC and to describe the data regarding the laterality, morphology, associated comorbidities and etiology. Heterogeneity was analyzed using the meta-regression method, and subgroup analyses were performed. 27 studies were selected from 2,610 references. The pooled prevalence estimate was 4.24 per 10,000 people, making it a rare disease based on WHO standards. Subgroup analyses revealed the highest CC prevalence in Asia, and an increasing prevalence trend through 2000. Other epidemiological characteristics showed CC tended to be bilateral, isolated, hereditary and in total/nuclear morphology. Huge heterogeneity was identified across most estimates (I2 > 75%). Most of the variations could be explained by sample size, research period and age at diagnosis. The findings provide suggestions for etiology of CC, improvements in screening techniques and development of public health strategies.