Background In the year 2019, around 5 million children under age five died and most of the deaths happened in developing countries. Though large numbers of deaths are reported in such countries, limited availability of data poses a substantial challenge on generating reliable estimates. Hence, this study aims to assess the prevalence and factors associated with under-five mortality in southeastern Ethiopia. Methods A register based cross sectional study was conducted from 1st September 2014 to July 2019 in Asella teaching and referral hospital. A total of 4901 under-five age children registered on the admission and discharge book of pediatric ward with complete information were included for the analysis. Data entry and analysis were conducted using Epidata Version 7 and SPSS version 21, respectively. Descriptive statistics were used to explore the characteristics of the study participants and their condition at discharge. Adjusted Odds Ratio (AOR) with its 95% Confidence interval and P-value less than 5% was used to decide the statistically significant association. Results The prevalence of under-five mortality among admitted children in Asella Teaching and Referral hospital was 8.7% (95% CI 7.91–9.50%). Post-Neonatal and Child mortality were found to be 9.1% and 8.18%, respectively. Moreover, large numbers of death (45.2%) were seen within the first 2 days of admission. Address (AOR:1.4(1.08–1.81)), HIV status (AOR:4.64 (2.19–9.8)), severe acute malnutrition (AOR:2.82 (2.03–3.91)), hypovolemic shock (AOR:4.32 (2.31–8.1)), type I diabetes with DKA (AOR:3.53(1.34–9.29) and length of stay in the hospital for ≤2 days (AOR: 4.28 (3.09–5.95)) as well as 3–4 days (AOR: 1.48 (1.02–2.15)) were among the identified predictors. Conclusions Though childhood mortality is swiftly decreasing, and access and utilization of health care is improving in Ethiopia, our study found large prevalence of under-five mortality, 8.7% and higher number of deaths in early days of admission. Improving the quality of service has a paramount importance in reducing the mortality and managing associated factors contributing to under-five mortality among admitted children.

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