Background: Neural tube defects are a major public health problem and substantially contribute to morbidity and mortality, particularly in low-income countries, including Ethiopia. There are a paucity of data on the magnitude and associated factors of neural tube defects in Ethiopia, particularly in the study setting. Objective: This study aimed to assess the magnitude of neural tube defects and associated factors among neonates admitted to the neonatal intensive care unit in Hiwot Fana Specialized University Hospital, Harar, Ethiopia. Methods: A hospital-based cross-sectional study was employed from October 2019 to January 2020. A total of 420 newborn-mother pairs were included consecutively. Data were collected using a face-to-face interviewer-administered questionnaire and clinical examination. Data were entered into Epi Data version 3.1 and analyzed using the statistical package for Social Sciences version 20.0 software. An adjusted odds ratio (AOR) with 95% confidence interval (CI) was used to identify the associated factors. A p-value <.05 was considered statistically significant. Results: The magnitude of neural tube defects was 5.71% (95% CI: 3.5-7.9). Approximately 83.5% of infants had spinal bifida and 16.5% anencephaly. In multivariable logistic regression analyses, preterm birth (32-34 weeks) (AOR= 3.84; 95% CI: 2.1,10.7), low birth weight (1000-1500 g) (AOR = 4.74; 95% CI: 1.8, 9.1), 1500-2500 g (AOR = 3.01; 95% CI: 2. 1, 13.2), maternal coffee consumption (AOR = 11.2; 95% CI: 3.1, 23.7), a history of abortion or stillbirth (AOR = 9.6; 95% CI:7.6,19.4), radiation exposure (AOR = 5.0; 95% CI:1.6,14.3), and intake of anticonvulsant drugs during pregnancy (AOR = 4.75; 95% CI: 1.5,16.2) were factors associated with neural tube defects. Conclusion: In this study, the burden of neural tube defects was 5.71% among neonates admitted to the neonatal intensive care unit, which was a public health concern. Increased attention to the monitoring of neural tube defects in eastern Ethiopia is crucial to improve birth outcomes in the study setting.