Pharmaceutical sector plays an important role in the medical and health system. Due to the globalization of the business, increasing demand and supply for drugs, growing regulatory requirements, all stages of the pharmaceutical supply chain (SC) are facing numerous predicaments. The traditional way of selection and evaluation of these predicaments is customarily done using technical information. This approach lacks the ability to project the burning issue that to be addressed first. Hence, a computing method of selecting the crucial issue from the existing issues is essential in a pharmaceutical supply chain. This paper considers seven different predicaments as criteria and five sub-criteria under each main predicament of a pharmaceutical supply chain. The intention of this project is to manifest the process of assessing and selecting the issue that to be addressed first by using multi-criteria decision making technique (MCDM), i.e., fuzzy analytical hierarchy process (FAHP). The criteria and sub-criteria weights are calculated and priority assessment of the predicaments is done by using FAHP. Finally, from the findings of this work, the predicaments are ranked from most important to least important. This gives information to the decision maker (DM) to solve the issue that is affecting the SC the most with respect to the others. © Published under licence by IOP Publishing Ltd.