This study aims to investigate the factors influencing value chain (VC) in pharmaceutical industry, as a very important sector in Iran. The research method is descriptive-analytical in term of method. The required data have been collected from the experts of a public joint stock company. Conducting the research, first the literature of VC is reviewed to identify the initial factors affecting on VC of pharmaceutical companies. In this Phase, 34 factors were identified in 8 categories including; institutional, industry, political, economic, social, technological, legal and environmental factors. In the next step, a primal evaluation of the initial factors by 14 experts of the research, resulted to the 20 more important factors which were used in the modelling process. Due to the need for fuzzy logic regarding subjective judgments in cause-effect relationships between factors, the fuzzy cognitive mapping (FCM) method in FCM expert software is used to visualize the relationships among these factors. The results show that technological capabilities, government policies, company resilience, financial strength, medicine price, sustainable waste management, cost of raw materials, production technology, cost of energy, R&D, operational efficiency, recycling capabilities, transportation cost, VC governance (coordination/ partnerships/ integration), consumer behavior and social (market) trends, environmental concerns about waste disposal internet of things (IoT) and connected devices, non-value-adding activities, import limitations and skilled human resources, respectively are the most influencing factors on pharmaceutical VC.