Background: Healthcare costs is one of the most studied issue in our days because of increasing demand and the aging of population. Final costs of medicines is one of the most important issue in patient treatment and determine its real value is an important task within hospitals. Simulation models and in this case system dynamics allows to build representations of reality considering the interaction of the whole variables that affect the system where first a causal loop diagram allows to represent and identify the interaction between variables for develop a stock flow diagram to determine the final results. Objective: Develop a simulation model that allows decision makers in Hospitals and Governments to identify the variables that affect the final cost of medicines and to determine the legal reimbursement allowed by national agencies. Methods: This paper presents a conceptual modeling framework using a causal loop diagram and a dynamic simulation model in the real case of a hospital in Colombia to explore how different internal charges for medicines affect the behavior of the final unit-dose cost of medicines, considering the complexity of the pharmaceutical system. We developed a simulation model to represent and characterize the pharmaceutical supply chain in a hospital and by using real data we validate the results of the model and conclude about the supply chain of medicines in Colombia using the legal regulations as a main factor of analysis. Results and conclusions: We found that in some cases the maximum reimbursement value is less than the final cost of medicines within the hospital, which means that hospitals lose money on the administration of medicines to patients. The benefit of this model is that with the result the hospital can determine the real final monetary value of medicines, including the different processes starting from the reception of the medicines, ending with the administration to patients.