Background: Neonatal period is the most the vulnerable time for survival of newborns. In Ethiopia, neonatal death remains increasing and requires extraordinary efforts and a novel intervention to reduced neonatal death as those deaths continue to occur in even hospital settings where there are the best neonatal care services. Despite many efforts done to improve the outcome of neonates admitted to hospitals; neonates continue dying in those settings. The causes of neonatal death in Ethiopia varies from place to place. So, identifying the causes of death in the study area is very important for prevention and treatment. The study aimed to assess the causes and factors associated with treatment outcomes. Methods: Institution-based cross-sectional study design was conducted among 707 randomly selected neonates from March 1 to 31, 2020. Data were extracted from medical records using a checklist adapted from WHO and neonatal registration book. The data were inserted into Epi-data version 3.1 and then exported into SPSS window version 22 for analysis. Bivariate and multivariate analyses were done to identify the association between independent variables and the outcome variable. Results: From 698 admitted neonates during 2 years period, 594 of them were improved and 104 of them were died. The proportion of neonatal death was 14.9% (95% CI:12.3,17.9). Neonatal sepsis, low birth weight and prematurity were the leading cause of neonatal death. Residency [ AOR=2.30, 95%CI: (1.3, 4.12)], low birth weight [AOR=2.52, 95%CI: (1.24,5.13))], respiratory distress syndrome [AOR =2.86, 95%CI:(1.11.7.35)], neonatal sepsis [AOR= 2.48, 95%CI: (1.40, 4.38)], and Neonates treated with phototherapy and oxygen [ AOR=0.22, 95%CI:(0.088,0.54)], [AOR= 0.47,95%CI:(0.22,0.99)] were factors associated with poor treatment outcome.Conclusion: The causes of neonatal death were mainly from preventable and treatable causes like neonatal sepsis, low birth weight, and prematurity in the study setting. Residency, low birth weight, respiratory distress syndrome, having neonatal sepsis, treatment with phototherapy, and treatment with oxygen were independent factors. The concerned bodies should give attention to neonates admitted to intensive care units by strengthening the quality of care given at the unit and strengthening early detection and prevention of neonatal problems during post-partum periods.