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Abstract Background Ethiopia witnessed an unprecedented decline in under-5 and neonatal mortalities since 2000. But, neonatal mortality still accounts for the largest proportion of under-five child mortality. Quality of service at hospitals may vary and determine the magnitude of neonatal mortality. Objective To assess the prevalence and associated factors of neonatal mortality among newborns Admitted to the Neonatal intensive care unit of Gandhi Memorial Hospital Addis Ababa, Ethiopia, 2019. Methods Institution-based cross-sectional study was conducted from November 1 to December 31, 2019. A sample of one in every 2 admitted patients was included in the study. our exclusion criterion was neonates who had no mothers or guardians and/or neonatal medical records incomplete for status at discharge. We used the Systematic random sampling technique to select the study participants. A pretested structured interviewer-administered questionnaire and a preliminary tested checklist were used to collect primary and secondary data respectively. Descriptive and summary statistics were performed. A binary logistic regression model was fitted and variables that had a P-value of < 0.05 in the multivariable model were considered statistically significant. Results A total of 570 neonates who have mothers were involved in the study giving a response rate of 98.8%. The prevalence of neonatal mortality was 7.7% (95% CI: 5.7, 9.8). Mothers' educational status (No education (AOR 3.37, CI 95%, 1.02–11.20), premature rupture of membrane (prolonged PROM) (AOR 5.59, CI 95%, 1.05–29.76), and birth weight less than 2500gm (AOR 3.23, CI 95%, 1.17–8.90) are the significant factors associated with neonatal mortality. Conclusion The prevalence of neonatal mortality at Gandhi memorial hospital was generally high. As our finding revealed, neonates who are underweight and whose mothers have no formal education as well as have prolonged PROM have higher odds of neonatal mortality. Thus, clinicians, policymakers, and program managers should give special attention to neonates of none educated mothers, mothers with prolonged PROM, and neonates with low birth weight.