A congenital encephalocele is the herniation of intracranial contents through skull defects of various sizes. Depending on the site, content, and size, it is associated with significant morbidity and mortality in children. There is a paucity of recent and comprehensive local clinical data regarding this anomaly. Understanding the peculiarities, clinical-pathologic profiles, and management challenges will help prevent and effectively manage congenital encephalocele to improve outcomes. This was a retrospective study of all cases of congenital encephalocele managed between July 2000 and December 2023 at a tertiary hospital in the southwest region of Nigeria. Relevant demographic, clinicopathological, and management data were retrieved and analysed. There were 31 females and 11 males. Their ages ranged from 3hours to 24years. Sixteen (35.3%) were delivered in a non-health facility. Birth asphyxia was reported in 5 babies. Few mothers (4.8%) used preconception folic acid. Anaemia (n = 5) and sepsis (n = 4) were the common preoperative morbidities. All patients had definitive surgery, with 18 operated on within the first month of life. Cerebrospinal fluid (CSF) leak was the most common postoperative complication and was significantly observed in the sincipital group (p = 0.018). Thirty-one patients (73.8%) presented for follow-up after surgery, and the mean follow-up duration was 26.6weeks. Mortality was recorded in a patient (2.4%) due to Klebsiella meningitis. Congenital encephaloceles are relatively common in our setting. Therefore, there is a need to address the associated poor maternal and neonatal health conditions. Early surgery can be performed with a favourable outcome.