IntroductionNeonatal mortality is a significant public health problem in Sub-Saharan Africa, particularly in Somalia, where limited data exists about this. Mogadishu, the densely populated capital, faces a high rate of neonatal mortality, but this has not been widely studied on a national level. Healthcare providers and policymakers are working to reduce newborn deaths, but a comprehensive understanding of the contributing factors is crucial for effective strategies. Therefore, this study aims to determine the magnitude of neonatal death and identify factors associated with it in Mogadishu, Somalia.MethodA multicenter hospital-based cross-sectional study was conducted to collect data from participants at 5 purposively selected hospitals in Mogadishu, Somalia. A well-structured, reliable, self-developed, validated questionnaire containing socio-demographic, maternal, and neonatal characteristics was used as a research tool. Descriptive statistics were used for categorical and continuous variables presented. Chi-square and logistic regression were used to identify factors associated with neonatal mortality at a significant level of α = 0.05.ResultsA total of 513 participants were recruited for the study. The prevalence of neonatal mortality was 26.5% [95%CI = 22.6–30.2]. In a multivariable model, 9 variables were found: female newborns (AOR = 1.98, 95%CI = 1.22–3.19), those their mothers who did not attend ANC visits (AOR = 2.59, 95%CI = 1.05–6.45), those their mothers who did not take tetanus toxoid vaccination (AOR = 1.82, 95%CI = 1.01–3.28), those their mothers who delivered in instrumental assistant mode (AOR = 3.01, 95%CI = 1.38–6.56), those who had neonatal sepsis (AOR = 2.24, (95%CI = 1.26–3.98), neonatal tetanus (AOR = 16.03, 95%CI = 3.69–69.49), and pneumonia (AOR = 4.06, 95%CI = 1.60–10.31) diseases during hospitalization, premature (AOR = 1.99, 95%CI = 1.00–3.94) and postmature (AOR = 4.82, 95%CI = 1.64–14.16) neonates, those with a birth weight of less than 2500 gr (AOR = 4.82, 95%CI = 2.34–9.95), those who needed resuscitation after delivery (AOR = 2.78, 95%CI = 1.51–5.13), and those who did not initiate early breastfeeding (AOR = 2.28, 95%CI = 1.12–4.66), were significantly associated with neonatal mortality compared to their counterparts.ConclusionIn this study, neonatal mortality was high prevalence. Therefore, the intervention efforts should focus on strategies to reduce maternal and neonatal factors related to neonatal mortality. Healthcare workers and health institutions should provide appropriate antenatal, postnatal, and newborn care.