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BACKGROUND: Neonatal hypothermia is a major cause of mortality. This study determined the prevalence and factors associated with neonatal hypothermia in two regional referral hospitals in Dar es Salaam, Tanzania. METHODS: Cross-sectional study was carried out between March and May 2021 at the Mwananyamala and Temeke Regional Referral Hospitals. Simple random and stratified sampling procedures were used to select study sites and proportionate population samples from each hospital respectively. Body temperature was measured within 90 minutes post birth; knowledge of the WHO guidelines on thermal protection of new-borns was collected from the mothers and health care providers using questionnaires. Logistic regression was used to assess associations between variables. SPSS version 25 was used to analyse the data and p < 0.05 was considered significant. RESULTS: Total of 296 mother-new-born pairs and 41 health care providers were enrolled in the study. 26 mothers did not consent for the study. 25.6% of the 270 studied neonates were hypothermic. Lack of skin-to-skin contact with the mother; early neonatal weighing and bathing increased likelihood of neonatal hypothermia. Knowledge of neonatal thermal protection among mothers and care-providers was inadequate. CONCLUSIONS: The prevalence of neonatal hypothermia among neonates in the referral hospitals is high. The findings suggest knowledge gaps of the WHO recommended guidelines on neonatal hypothermia are associated with neonatal hypothermia. Efforts to increase awareness of the WHO recommended thermal protection guidelines are needed.