Background Hypoxic Ischemic Encephalopathy (HIE) remains a significant cause of death and neuro-developmental deficits among children, especially in resource limited settings. Therapeutic hypothermia which is the mainstay of treatment for moderate to severe hypoxic ischaemic encephalopathy in developed countries, is not widely practiced in low resource settings and the available data is limited. We aimed to determine the short term outcomes and factors associated with survival among newborn infants with moderate to severe hypoxic ischaemic encephalopathy treated with therapeutic hypothermia at St. Francis Hospital, Nsambya. Methods Retrospective cohort study of 81 newborn infants with moderate to severe HIE who were 36 weeks and above that were cooled from June 2016 to February 2019, at St. Francis Hospital, Nsambya, Kampala, Uganda. Data on maternal and infant characteristics, clinical outcomes were extracted from the HIE registry and HIE follow up forms. Descriptive analysis was done to get the patient characteristics. Survival analysis was done to compare outcome among the groups of infants with significant factors at bivariate analysis. Multiple cox proportional hazards regression analysis was done to determine the factors independently associated with survival. Results The proportion of newborn infants who survived was 68/81(84%), (95%: CI: 0.74, 0.91).The factors associated with survival were a Thompson score of 7 to10 at initiation of cooling(HR: 0.07, 95% CI: 0.01, 0.94) and at 24 hours of cooling(HR:0.03, 95%CI: 0.004, 0.21), being born within the hospital providing therapeutic hypothermia (HR: 0.26, 95% CI: 0.07, 0.94) and not needing mechanical ventilator (HR: 0.03, 95% CI: 0.01, 0.14) or inotropic support.(HR: 0.13, 95%CI: 0.04, 0.38). The median time to attainment of full cup feeds was 6 days, with the majority 43/68(63%) attaining full feeds from 5 to 8 days. The median time to discharge was 7 days, and the median time to death was 3 days. The median Thompson score at discharge was 1 and at death was 16 Conclusion The survival rate of cooled infants in our setting at 84% is comparably high. The majority of infants have normal neurology at discharge.