Summary Background Strategic purchasing has been introduced as a key strategy for solving the problems faced by insurance companies. In Iran, the government has mandated the Iran Health Insurance Organization (IHIO) to implement this strategy. However, there are serious challenges to achieving that. The present study aims to identify these challenges. Methods In this qualitative study, a semi‐structured interview was conducted on 27 health managers and experts at the national level. The dimensions of the A. Preker model were used to analyze the data. Results Challenges of strategic purchasing in the IHIO were categorized into five concepts—political economy, policy design, organizational structure, organizational environment, and management capacity; within these concepts, 22 challenges were identified. Conclusions Improving strategic purchasing in Iran requires adopting a coherent approach and taking into account all the affecting factors. By revising some policies, and modifying and defining the rules needed to solve the infrastructural problems, the success of strategic purchasing can be obtained.