Background There are limited population-based studies on congenital heart disease (CHD) in the pediatric population in Africa. Technological advancements in diagnostic tools have resulted in multiple echocardiographic studies in hospital settings. We aimed to determine the prevalence of CHD in both settings (population-based and hospital based) followed by comparing the two estimates for a difference. Methods We systematically searched PubMed, Google Scholar, African Journals Online, and African Index Medicus for eligible studies from 1992 through 2022. We performed a meta-analysis using the random-effects model. Results We selected 42 studies; 10 population studies with 1,011,163 participants, and 32 hospital-based studies with 605,268 patients for the analyses. The population and hospital-based prevalence were 5.12 versus 12.63 per 1,000 population of children ( P = .007). Ventricular septal defect was the most common type of CHD in both settings (0.61 vs 1.88 per 1,000), followed by atrial septal defect (0.26 vs 0.68 per 1,000). Tetralogy of Fallot was the most common cyanotic heart lesion in both settings (0.08 vs 0.52 per 1,000). Conclusions The population-based prevalence of CHD was significantly lower than the hospital-based prevalence (5.12 vs 12.63 per 1,000 population of children). Juxtaposing these two prevalence estimates against each other can be a reasonable alternative to quantifying the contemporary burden of CHD in the pediatric population of Africa. Moving forward, efforts should bolster awareness of CHD in Africa, and further advocacy for children with CHD should be a priority on the continent.