Pharmacoeconomics can play a very important role in decision-making for healthcare structures. In fact, it consists of economic evaluation of drugs and treatments for specific diseases. Several techniques exist for this, mainly based on traditional management and financial methods as, for example: cost-minimization analysis, cost-benefit analysis, cost-effectiveness analysis or cost-utility analysis. The present paper proposes the use of agent based process simulation as an additional tool to assess the pharmacoeconomic analysis, in which to incorporate traditional financial tools. This technique allows to compare different treatments ceteris paribus, that is by simulating the effects of different drugs and treatments on the same patient, by comparing both the medical effects and the economic and financial effects. Last, the paper proposes the case of ozone therapy as a powerful use case for this simulative approach, since ozone, a natural gas with antibacterial and anti-inflammatory properties, can successfully be used to treat many diseases as an alternative to other drugs and treatments.