Background: The implementation of different reimbursement methods has various positive and negative effects on the health system of different countries. Identifying the challenges of these methods is essential to improve these reimbursement methods and modify them if required. This article aimed to qualitatively assess the challenges of current hospitals' payment systems in the Iranian health system and determine the required solutions for modifying these payment systems. Methods: This qualitative study was conducted in 2019. Semi-structured interviews were conducted recruiting 20 experts including operational, middle and top managers working in three different levels of health systems. Data collection was continued until it reached a saturation point. MAXQDA 10 was used for data analysis. The data content analysis method was used to analyze the data and the themes and categories were determined. Results: The challenges of the payment systems were categorized into four main themes regarding policy, cost, regulatory and functional challenges, and 15 sub-themes. The findings related to the proposed strategies were presented in six main themes consisting of legal solutions, structural reform, cost, quality improvement, service provider and client, and monitoring and evaluation; and 12 sub-themes. Conclusion: This study showed that the health systems in Iran face various structural and procedural challenges in terms of reimbursement mechanisms. Therefore, it is recommended that policymakers pay attention to these challenges before making any changes. Using hybrid payment systems can be one of the proper solutions.