Background:Congenital anomalies, including those of the central nervous system (CNS), are among the leading causes of morbidity, mortality, and fetal loss.Objective:To determine the prevalence and associated factors of CNS congenital anomalies in children.Methods:A cross-sectional retrospective study of children managed with CNS anomalies was undertaken. Relevant clinical data of identified cases based on standard case definitions were retrieved from their case record files. Data were analyzed using SPSS 20.0 while the level of statistical significance was set at P < 0.05.Results:Seventy-two cases of CNS anomalies were identified over the period under review; out of 7329 total pediatric admissions giving a prevalence of 0.98%. Spina bifida cystica, 49 (68.0%) was the most common of the five anomalies seen followed by congenital hydrocephalus 11 (15.3%). Fifty-seven (79.2%) of the mothers did not take periconceptional folic acid supplementation (P < 0.05) whereas 25 (34.7%), 6 (8.3%), and 1 (1.4%) reported history of febrile illness in the first trimester of pregnancy, alcohol use, and diabetes mellitus in pregnancy, respectively. Majority of the cases of spina bifida cystica (30 [61.2%]) seen had corrective surgeries while the overall case fatality rate was 1 (1.4%).Conclusions:Spina bifida cystica was the most common anomaly of the CNS seen in this study and majority of the mothers of affected children did not take periconceptional folic acid supplementation (P < 0.05). Efforts should be made to create awareness and apply adequate preventive health education models including the use of periconceptional folic acid supplementation as well as the provision of access to standard prenatal care to at risk mothers.