Introduction. Neonatal hypothermia is the reduction in the body temperature of the newborn (less than 36.5°C). It is a global problem in neonates born both at hospitals and homes, but it showed a higher prevalence in developing countries (>90%). Although hypothermia is rarely a direct cause of death, it contributes to a substantial proportion of neonatal mortality globally. Objective. To assess neonatal hypothermia and associated factors among newborns admitted in the NICU of Dessie Referral Hospital. Methods and Materials. An institution-based cross-sectional study was conducted from March 15 to May 30, 2018. The data was collected from the mother and the chart of the newborn using a semistructured questionnaire. Data were cleaned, coded, and entered in EPI-info version 7.1.2.0 then exported to Statistical Package for Social Sciences (SPSS) version 20 software for analysis. Descriptive statistics were used to summarize the data. Bivariate and multivariate logistic regression and crude and adjusted odds ratio with their 95% confidence interval were computed. Finally, p value < 0.05 was used to identify variables that had a significant association with neonatal hypothermia. Result. The proportion of neonatal hypothermia in the study area was 66.8%. Preterm delivery (AOR=2.6, 95% CI: 1.1, 6.2), no skin-to-skin contact within 1 hour of delivery (AOR=3.0, 95% CI: 1.3, 7.8), delivered at night time (AOR=2.0, 95% CI: 1.02, 4.0), and neonates who had resuscitation (AOR=2.9, 95% CI: 1.1, 7.2) showed significant association with neonatal hypothermia. Conclusion. In this study, the proportion of hypothermia was high. Preterm delivery, no skin-to-skin contact within 1 hour, night-time delivery, and having resuscitation were significantly associated with neonatal hypothermia. Therefore, special attention is needed for the thermal care of preterm neonates and neonates delivered at night time. Furthermore, there should be strict adherence to cost-effective thermal care recommendations like warm resuscitation and skin-to-skin contact.