Background Hypoglycaemia is a common metabolic abnormality seen in neonates that can cause preventable death. Its overall incidence has been estimated to be 1 to 5 per 1,000 live births, with higher incidence in at-risk populations. There is limited data regarding its prevalence and risk factors in developing countries like Ethiopia. Therefore, this study was aimed to determine the prevalence and risk factors of neonatal hypoglycaemia in neonatal intensive care unit (NICU) at Saint Paul’s Hospital Millennium Medical College (SPHMMC), Addis Ababa, Ethiopia. Methodology A cross sectional study was conducted from June 17 to August 3, 2018 at SPHMMC, NICU. Neonates whose age was less than 48hrs and admitted to NICU were enrolled. Sociodemographic, maternal and neonatal factors were collected using structured questionnaire. Blood glucose was measured using glucometer with a test strip. Random blood glucose level < 47mg/dl was taken as a cut-off point to define hypoglycaemia. The data was entered and analysed using SPSS version 20. Results Neonatal hypoglycaemia was detected in 25% (49/196) of the neonates. Birth weight, duration of labor, maternal age, time of feeding initiation, hypothermia and respiratory distress syndrome were associated with hypoglycaemia. From these factors, maternal age, birth weight and hypothermia were found to be independent predictors of the outcome. Conclusion Hypoglycaemia was prevalent in neonates admitted to the NICU of SPHMMC and was associated with low birth weight and hypothermia. These findings calls for early detection of hypoglycaemia, prevention of hypothermia and early initiation of feeding to prevent neonatal morbidity and mortality.