Introduction Congenital heart defects (CHDs) are the most common congenital defects and accounts for nearly one-third of all major congenital anomalies. It is the leading causes of birth defect-associated morbidity, mortality, and medical expenditures. Of all CHD types, ventricular septal defect (VSD) and atrial septal defect (ASD) accounted 51% of cases with an increasing trend over time. Objective The aim of this review is to estimate the pooled prevalence of ventricular septal defect and congenital atrial septal defect among congenital heart diseases patients in East African context. Methods Using PRISMA guideline, we systematically reviewed and meta-analyzed studies that examined the prevalence of Ventricular septal defect and atrial septal defect in East Africa, from Medline (PubMed), Cochrane Library, HINARI, and Google Scholar. A weighted inverse variance random-effects model was used to estimate the pooled prevalence of ventricular septal defect and atrial septal defect. Results A total of 2323 studies were identified; 1301 from PubMed, 12 from Cochrane Library, 1010 from Google Scholar and 22 from other sources. The pooled prevalence of ventricular septal defect and atrial septal defect in East Africa was found to be 29.92% (95% CI; 26.12–33.72; I2 = 89.2%; p<0.001), and 10.36% (95% CI; 8.05–12.68; I2 = 89.5%; p<0.001) respectively. Conclusions and future implications Based on this review, the pooled prevalence of VSD and ASD is still high and alarming; this signifies that the emphasis given for congenital heart defect in East African countries is limited. Special attention and efforts should be applied for early detection to prevent serious complications and for a better prognosis of all forms of CHD. A screening program for CHD should be instituted during the perinatal period. Furthermore, early referral of suspected cases of congenital cardiac anomalies is mandatory for better management till the establishment of cardiac centers in different regions of the continent.