BACKGROUND: Despite the implementation of a free healthcare policy for pregnant women and children under five since 2006, neonatal mortality remains high in Burundi. Indeed, twenty-one neonates per 1,000 live births died in 2019. This study aimed to assess neonatal survival and identify factors associated with neonatal mortality in one tertiary hospital of Bujumbura, Burundi. METHODS: We recruited 885 babies whose births occurred between October and December 2020 in Kamenge Teaching Hospital of the University of Burundi and followed them over four months. We applied life table methods and implemented the Cox proportional hazard regression model to evaluate neonatal survival and determine factors associated with neonatal mortality. RESULTS: Among 885 live births, 30 neonates died and 133 were lost to follow-up, resulting in a neonatal mortality rate of 36.65 per 1,000 live births. Notably, 90% of neonatal deaths occurred within the first week of life, with 40% within the first 24 h. The leading causes of death included complications related to prematurity (60%), asphyxia (13.33%), infections (13.33%), and congenital malformations (13.33%). Mortality increases with severe prematurity (AHR: 14.60, 95%CI 5.83-36.54), fewer ANC (AHR: 6.67, 95%CI 1.54-29.25), and Apgar score below 6 at five minutes (AHR: 4.37, 95%CI 1.66-11.44). CONCLUSION: Neonatal mortality remains high, predominantly driven by preventable and curable complications. Further research is needed to explore this subject on a large scale to inform targeted interventions.