The demand for accurate and effective cool chains has been expected to increase, especially for pharmaceuticals in the air freight industry. However, several problems and challenges remain such as cool chain breaks and cool storage capacity constraints while there are rarely routine systems in place for consistent insight into the operational quality of such systems. Besides, the concept of a DT has received increasing attention in the literature, while a multitude of applications have been found in fresh cool chains. Therefore, the DT concept has been applied to a pharmaceutical cool chain for operational quality improvement. Firstly, a novel operational quality metric has been proposed: the OCCE. Consequently, a cool chain at KLM Cargo has been studied and modelled by means of the DES technique in order to derive a virtual representation. Consequently, the DT concept has been applied through the implementation of a decision support module for cool storage decision-making. The model implementation has shown that the cool chain operational quality has been improved while the average exposure of freight has decreased.