OBJECTIVE: To assess the impact of secondary and tertiary level neonatal interventions on neonatal mortality over a period of 11 years. DESIGN: Interrupted time series analysis. SETTING: Nsambya Hospital, Uganda. INTERVENTIONS: Neonatal secondary interventions (phase I, 2007-2014) and tertiary level interventions (phase II, 2015-2020). PARTICIPANTS: Neonates. PRIMARY AND SECONDARY OUTCOME MEASURES: Primary outcome: neonatal mortality. SECONDARY OUTCOME: case fatality rate (CFR) for prematurity, neonatal sepsis and asphyxia. RESULTS: During the study period, a total of 25 316 neonates were admitted, of which 1853 (7.3%) died. The average inpatient mortality reduced from 8.2% during phase I to 5.7% during phase II (p=0.001). The CFR for prematurity reduced from 16.2% to 9.2% (p=0.001). There was a trend in reduction for the CFR of perinatal asphyxia from 14.9% to 13.0% (p=0.34). The CFR for sepsis had a more than a twofold increase (3%-6.8% p=0.001) between phase I and phase II. CONCLUSION: Implementation of secondary and tertiary neonatal care in resource-limited settings is feasible. This study shows that these interventions can significantly reduce the neonatal mortality, with the largest impact seen in the reduction of deaths from perinatal asphyxia and prematurity. An increase in sepsis related deaths was observed, suggesting emphasis on infection control is key.