Unpredictable changes in the current business environment have made organizations pay attention to the concept of agility. This concept is a key feature to survive and compete in turbulent markets while considering customers’ fluctuating needs. An organization’s agility is a function of its supply chain’s agility. The present study offers a System Dynamics (SD) model for Iran’s Pharmaceutical Supply Chain (PSC). The model is presented in three steps. First, the Supply Chain (SC) indicators were extracted based on theoretical foundations and literature review results. Second, an SD model of the PSC was extracted in the context of the COVID‑19 pandemic with the necessary analyses. Finally, the desired outputs and strategies were obtained by conducting a case study. The results indicated that the PSC’s highest agility could be guaranteed by the simultaneous implementation of three strategies: investment, Human Capital Development (HCD), and accelerated completion of ongoing projects on a priority basis. According to these results, the organization had better determine the amount of capital and workforce required for ongoing projects, then design funding solutions to implement these projects and implement them according to the projects’ priority.