In relation to the logistics processes created and operated by companies, the choice of the optimal packaging system is a rightful social and industrial expectation. Choosing the right packaging system can reduce the environmental impact and make logistics processes more efficient. These aspects are key factors for the competitiveness of companies. It can be concluded that in practice, the selection of a right packaging system in a company is mostly based on experience. In the literature, the choice of such a system is based on the analysis of the processes of a single company, i.e., no method has been developed to integrate the processes of several companies to optimize the choice of a packaging system. Consequently, several losses can occur, both at the system boundaries and within the company processes, for example, losses from unnecessary material handling, operations, product damage, etc. The aim of this paper is to present the concept of an innovative packaging management framework that can be used to select the optimal unit load handling equipment based on the company’s needs defined by simulation-based optimization. The application of the concept is also presented through a case study. It is demonstrated that the application of the developed concept can be a significant step towards the realization of sustainable supply chains through more efficient process design.