Background: Societal resilience against disasters and mass casualty incidents (MCIs) depends significantly on robust disaster organizations and systems established during the preparedness phase. In Türkiye, the Ministry of Health’s Health Disaster Coordination Center (SAKOM) is a key entity in managing the health impact of disasters. This study examines the establishment, organization, and current systems used by the SAKOM, revealing the dynamics of a national medical disaster management system. Methods: A qualitative research approach was used to analyze official documents published by the Republic of Türkiye Ministry of Health between 2009 and 2024 using the Ready materials, Extract data, Analyse data, Distil (READ) method. Results: Twelve of twenty-two documents published by the Ministry of Health over fifteen years were analyzed. Documents containing repetitive information and those not directly related to the SAKOM were excluded. Twelve key documents were identified as primary sources. Three main themes and six sub-themes were identified. The first theme addressed the SAKOM purpose, historical development, and guidelines, including the structure of Provincial SAKOMs. The second theme is a detailed event reporting criteria, the SAKOM activation processes, and the organization of 112 Emergency Call Centers. The role of the Health Command and Control Center in the activation and incident tracking was highlighted. The third theme analyzed the electronic systems used by the SAKOM, such as the Incident Management System and the Emergency Health Automation System, covering incident management and data integration processes. Conclusions: This study provides insight into the SAKOM’s operational principles and its role in Türkiye’s health management during disasters and MCIs, contributing to global knowledge on disaster management systems.