Hospitals are increasingly challenged by the need to enhance supply chain performance, particularly in managing patient flows across various care units such as emergency departments. Inefficiencies in these flows can significantly impact care quality and patient satisfaction. This study proposes a modeling and simulation approach using Colored Petri Nets (CPNs) to analyse and improve hospital operations. Focusing on an emergency department, we developed a CPN-based model that simulates patient trajectories while incorporating various types of disturbances, such as sudden surges in patient arrivals and resource availability constraints. Through simulation, we identified key bottlenecks—especially in waiting areas—that contribute to delays in patient care. The results demonstrate the effectiveness of CPNs in enabling a detailed and dynamic analysis of complex healthcare systems. This approach provides actionable insights into improving the flexibility and responsiveness of hospital processes, ultimately reducing wait times and enhancing patient satisfaction. Our findings highlight the potential of CPNs as a powerful tool for understanding and managing the dynamic behavior of hospital supply chains under variable and uncertain conditions.