One of the main characteristics of health systems and pharmaceutical supply chains is their significant costs in the public sector, which has forced governments and companies active in this field to find ways to reduce costs. In this paper, the deterioration of imported pharmaceutical items is investigated as one of the challenges of the supply chain of pharmaceutical firms. Specifically, the micro, small medium enterprise (MSME), and a collaborative strategy to reduce its costs is presented. The technical solution of the cooperative strategy is the formation of a partnership alliance between the foreign patent holder of brand drugs and a domestic manufacturer through an exclusive license contract in the local country. This leads to a significant reduction of costs in the distribution network of the pharmaceutical supply chain. On the other hand, supply chain management techniques in the cooperative strategy provide the necessary motivation for its practical implementation by splitting fair profits between producers and other members, namely local government, distributors, and pharmacies. For these purposes, a cooperative game theory-based contract is utilized to set the parameters of the license agreement, and then a profit-sharing mechanism is introduced that splits the benefits of cooperation among the supply chain members based on their afforded costs. The most important contribution of the current research is to propose an integrated framework that combines the logistics network models, valuation methods, and profit split mechanisms that embody more facts from real-world problems than separate models in this regard in previous studies. Moreover, results of the proposed strategy in the supply chain of a drug for thalassemia patients in Iran indicate the effectiveness of the proposed strategy in reducing costs and deterioration. Further, it is shown that the higher the ordering costs of the imported drugs, the lower the market share of the patent holder, and the lower the financing expenses of the cooperative alliance, the more efficient is the proposed strategy.