Background: The neonatal period, encompassing the first 28 days of life, is a critical phase for newborn survival. Neonatal mortality refers to the death of newborns within the initial four weeks of life and constitutes a significant portion of child mortality under five years old, accounting for 38% of these deaths in the developing world. The causes of neonatal mortality vary across different regions. Objective: The aim of this study is to assess the prevalence, causes, and associated factors of neonatal mortality among neonates admitted to Asella Referral and Teaching Hospital in Asella, Ethiopia, in 2024. Method: A facility-based retrospective cross-sectional study was conducted among neonates admitted to Asella Referral and Teaching Hospital from July 7, 2020, to July 7, 2023. Participants were selected using a systematic random sampling method. Data collected were entered into Epi Data Version 3.1 and analyzed using SPSS Version 26. Descriptive analysis was performed for all independent variables. Variables with a p-value < 0.25 in bivariable logistic regression analysis were further analyzed using multivariable logistic regression. A significant association between independent variables and the outcome variable was considered at a p-value < 0.05 in the multivariable regression analysis. Results: This study included 194 neonates, with a neonatal mortality prevalence of 13.9%. The leading causes of neonatal mortality were birth asphyxia (22.1%), meconium aspiration syndrome (14.8%), and neonatal sepsis (11.1%). Factors such as obstructed labor [AOR=3.5: 95% CI (1.2–10.7)], instrumentally assisted vaginal delivery [AOR=3.5: 95% CI (1.03–11.9)], pregnancy-induced hypertension [AOR=2.0: 95% CI (1.2–14.5)], and lack of antenatal care follow-up [AOR=3.2: 95% CI (1.1–9.9)] were identified as predictors of neonatal mortalities (p <0.05). Conclusion: The study revealed a high prevalence of neonatal mortalities. Obstructed labor, instrumentally assisted vaginal delivery, pregnancy-induced hypertension, and inadequate antenatal care follow-up were significant predictors of neonatal mortality. Improvements in obstetric care quality, antenatal follow-up, and emergency obstetric services are crucial to reducing neonatal mortality rates in the study setting.