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Background Childhood mortality rates remain high in sub-Saharan Africa. This study aimed to assess the causes and associated factors of pediatric emergency mortality at the Sourô Sanou University Hospital of Bobo-Dioulasso. Methodology This was a cross-sectional study with prospective collection from June to August 2020. We documented and analyzed demographic and clinical characteristics by means or proportions. Logistic regression was performed to identify the factors associated with childhood mortality. Results From 618 pediatric patients admitted to pediatric emergency unit, 80 (12.9%) were documented as death outcomes. The mean age was 34.10 ± 36.38 months. The male sex represented 51.25%. The main diagnoses were severe malaria (61.25%), acute gastroenteritis (11.25%) and pneumonia (10%); 48.75% of the patients were malnourished and only 55% were fully immunized. The average length of hospitalization was 2.73 ± 3.03 days. Mortality was a strongly significant association with late come to the emergency unit (AOR = 1.11, CI = 1.04–1.18), young maternal age (AOR = 0.95, CI = 0.92-0.99) and incomplete vaccination (AOR = 1.94, CI = 1.13-3.31). Conclusion The in-hospital mortality rate was 12.94%; younger maternal age, delay in consultation, unimmunized or incompletely immunized status and shorter hospital stays were significantly associated with death. [ABSTRACT FROM AUTHOR]