There is a huge burden of neural tube defect (NTD) in Ethiopia, and surgical management is not readily available. We aimed to assess the clinical profile and hospital outcome of children with NTD that were operated in Hawassa University Comprehensive Specialized Hospital, Hawassa, Ethiopia. A retrospective cross-sectional study on 250 children with NTD that were treated in a tertiary hospital from March 2016 to May 2020 was conducted to describe the clinical profile and treatment outcome at discharge. Logistic regression analysis was carried out to evaluate factors that determine mortality. Out of the 250 children, 50.4% were male. Myelomeningocele was the most common type of NTD (77.2%) followed by meningocele (10.4%). Only 3 mothers (1.2%) received periconceptional folic acid. Prenatal diagnosis of NTD was made in only 22 (8.8%) cases. 52.8% of the NTDs were ruptured at presentation and 50.8% had associated sepsis. At presentation, 42.4% were ≤72 hours of age and only 18 neonates (7.2%) were operated within 72 hours of admission. 54% had associated hydrocephalus, 31.6% had Chiari II malformation and 19.6% had club foot. Surgical site infection, post MMC repair hydrocephalus, and meningitis were seen in 8%, 14% and 16.8% of the participants, respectively. The mean duration of hospitalization was 24 ± 14.4 days. Twenty patients (8%) died before discharge from hospital. Prematurity [AOR: 26 (95% CI: 8.01, 86.04), P < 0.001] and the presence of meningitis [AOR: 3.8 (95% CI: 1.12,12.9), P = 0.03]were determinants of mortality. NTDs are substantial health problem in this part of the country. Periconceptional folic acid supplementation is almost non-existent. Prenatal detection of NTDs is very low and management is delayed in the majority of cases. Myelomeningocele is the most common type of NTD. There is high in-hospital mortality, and prematurity and the presence of meningitis are its determinants.