Background and objective Encephaloceles are considered to be a spectrum of neural tube defects with a herniation of the brain and the meninges through a bony skull defect to the exterior. Methods This retrospective and prospective study was carried out on 30 patients with congenital encephaloceles either vault or basal. The risk factors and the prognostic factors were assessed. Results There was a statistically significant association between the content of the sac, outcome and seizures. There was a presence of neural tissue associated with worse outcome and seizures. There was a statistically significant association between the size of the sac and outcome with seizure. There was a statistically insignificant association between site of defect and parent consanguinity, folic acid intake, drug history, seizures, outcome, gender, family history and a statistically significant association between the site of the sac and hydrocephalus. There was a statistically significant association between the outcome and presence of Hydrocephalus, microcephaly and seizures. Conclusions There was statistically significant association between the worst outcome and presence of hydrocephalus, microcephaly and seizures, and there is correlation between site of the defect in occipitocervical region and development of hydrocephalus.