Globally, neonatal hypoglycemia is a common child health problem and significantly contributes to morbidity and mortality, with its impact being particularly detrimental in developing countries. Although being a prevalent metabolic condition, it is frequently overlooked. Furthermore, the problem is not adequately studied in Ethiopia, as seen by a few published studies on the topic, highlighting the lack of knowledge about its determinants. This study aims to assess the determinants of neonatal hypoglycemia among neonates admitted to neonatal intensive care units of public hospitals in Wolaita Zone, Southern Ethiopia, 2023. An institution-based unmatched case-control study design was conducted among 249 (83 cases and 166 controls) participants. Data were collected from 29 March to 23 May 2023 using a pretested chart review extraction tool/checklist. A consecutive sampling method was used for participant selection. Data were analyzed using Statistical Package for Social Science version 25. Binary logistic regression analysis was used to identify the determinants of neonatal hypoglycemia, and statistical significance was declared at P < 0.05. A total of 83 cases and 166 controls were included in the study. The following factors were significantly associated with neonatal hypoglycemia: preterm neonates [adjusted odds ratio (AOR) 4.888 (95% confidence interval, CI, 1.113-21.478)], age of the neonate at admission (3-5 h) [AOR 4.205 (95% CI 1.852-9.547)], hypothermia [AOR 5.485 (95% CI 2.360-12.748)], late initiation of breastfeeding [AOR 6.229 (95% CI 2.665-14.599)], mode of delivery [AOR 5.034 (95% CI 1.688-15.011)], and small for gestational age [AOR 3.645 (95% CI 1.286-10.330)]. In the current study, numerous determinants of neonatal hypoglycemia have been identified. Therefore, it is crucial to give due emphasis to providing comprehensive health education to mothers regarding effective breastfeeding methods, strategies to avoid neonatal hypoglycemia, and the various factors that heighten its likelihood. In addition, healthcare professionals should emphasize implementing preventive measures to prevent this grave condition.