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Recent public health emergencies, including the COVID-19 pandemic and large-scale natural disasters, have exposed vulnerabilities in pharmaceutical and health-product supply chains. These events demonstrate that preparedness relies not only on surveillance or clinical capacity but also on the effective management of medicine logistics systems. This scoping review aimed to identify existing assessment tools for public health emergency (PHE) preparedness and health supply chain (HSC) management and to develop an integrated framework that links these two areas to support more comprehensive evaluation of system readiness. A scoping review was conducted following the Arksey and O’Malley framework and PRISMA-ScR guidelines. MEDLINE (PubMed) and Scopus were searched for records published between January 2002 and July 2024, complemented by grey literature searches and expert consultation. Predefined inclusion and exclusion criteria were applied, and data were mapped using the Flower Framework, which combines domains of PHE management with pharmaceutical supply chain functions. Of 3,965 records identified (3,920 from databases and 45 from grey literature), 23 assessment tools met the inclusion criteria. Fourteen tools were developed in academic or research settings and nine in policy or programmatic grey literature. Instruments focused on PHE preparedness tended to emphasize governance, coordination, and core public health capacities, whereas HSC tools highlighted forecasting, procurement, inventory management, and warehousing. Only a few instruments bridged both perspectives. This scoping review reveals that no single instrument currently provides a comprehensive assessment of pharmaceutical system readiness across governance, regulatory, and operational dimensions. While existing tools offer situational benchmarking, they often fail to capture functional synergy and pharmaceutical-specific requirements like cold-chain integrity and regulatory constraints. Synthesizing findings through the Flower Framework, this study proposes an integrated model that bridges the gap between static capacity and real-world resilience, emphasizing the need for functional evaluations—such as stress tests and simulations—to more accurately reflect system adaptability during crises.