Background: Human Resource Management Practices (HRMPs) are increasingly recognized as a strategic driver of organizational performance (OP) in healthcare systems worldwide. In fragile contexts such as Somalia, HRMPs remain underdeveloped due to weak governance, political instability, and reliance on donor-driven initiatives. This study examines the effect of HRMPs— including recruitment and selection, training and development, performance appraisal, and compensation—on the organizational performance of hospitals in Mogadishu. Methods: A quantitative, descriptive research design was adopted. Data were collected from 223 healthcare professionals—including administrators, HR managers, doctors, nurses, and support staff—through structured questionnaires. Snowball sampling was employed, and Partial Least Squares Structural Equation Modeling (PLS-SEM) using Smart PLS software was applied to test relationships between HRMPs and organizational performance. Reliability and validity were confirmed using Cronbach’s alpha, composite reliability, factor loadings, and average variance extracted (AVE). Results: Findings revealed that HRMPs significantly predict organizational performance, with recruitment and selection and training and development emerging as the strongest contributors. The measurement model demonstrated robust reliability and validity, with Cronbach’s alpha and composite reliability values above 0.70 and AVE values exceeding 0.50. The structural model showed that HRMPs explained 54.1% of the variance in organizational performance (R² = 0.541). Hospitals with structured HR practices achieved better staff productivity, patient satisfaction, and internal efficiency compared to those relying on informal or donor-dependent approaches. Conclusion: The study concludes that effective HRMPs play a critical role in enhancing organizational performance in Somali hospitals. Institutionalizing transparent recruitment, continuous training, equitable compensation, and performance appraisal systems is essential for sustainable healthcare delivery. The findings contribute to theory and practice by extending HRM literature to fragile health systems and providing context-specific recommendations for hospital administrators, policymakers, and development partners.