Background Perinatal asphyxia is one of the preventable and treatable causes of neonatal mortality. However it is the fifth largest cause of under-five mortality. There are both long-term and short-term neurodevelopmental consequences of perinatal asphyxia, which can result in disability or even death. Even though management advancements, it remains one of the key public health issues in underdeveloped countries, including Ethiopia. Comorbidities are also understated therefore adequate information regarding the incidence of death and its predictors is required. Methods A four-year retrospective follow-up study was conducted from October 03 to November 02, 2022. From a total sample size, 616 data were collected by nurses reviewing charts using Kobo Toolbox software. Data was exported to STATA Version 14 for analysis. Cox proportional hazard assumption was checked and the model for the data was selected by Akaike Information Criteria. Finally, an adjusted hazard ratio with 95% CI was computed, and variables with a P-value < 0.05 in the multivariable analysis were taken as significant predictors of death. Result The overall incidence of mortality was 38.86/1000 days (95%CI: 33.85–44.60). The median time of follow-up was 15 days (95% CI: 14–20). The proportion of deaths was 202 (32.79%, 95% CI: 29.18–36.61) among neonates with perinatal asphyxia. While distance from health facility > 10 KM is (AHR: 2.25; 95%CI: 1.60–3.17), direct oxygen (AHR = 1.83; 95% CI: 1.35–2.48), APGAR score < 3 at fifth minute (AHR = 2.63; 95% CI: 1.03–6.73), prolonged ROM (AHR = 1.41; 95% CI: 1.02–1.94), and stage III HIE (AHR = 2.02; 95% CI: 1.18–3.47) were a predictors of mortality, among neonates with perinatal asphyxia. Conclusion The study found that, neonatal mortality among perinatal asphyxia remains high. Therefore, in order to reduce neonatal mortality among asphyxiated neonates, reducing prolonged ROM, APGAR score < 3 at fifth minute, using direct oxygen, stage III HIE, and a place of residences more than 10KM away from health facility.