Abstract Performance-based budgeting is one of the key factors of today's organization efficiency. Economically, "budget philosophy" is due to the existence of a "total contradiction" that is in every society and a curtesy of "knowledge economy" is completely created. Based on experts’ opinions, Lack of understanding and restructuring the issue of the budget is one of the operational problems of the performance-based budgeting of an organization. In this study, we decided to use the soft systems methodology to deal with budget issues that have components of social, political and human. In this methodology, the problem is a part of a single system rather than a problem to be investigated. Also, after structuring the problem and identifying preferences of experts, hierarchical clustering was applied to prioritize indicators. Therefore by combining these two approaches for Iran Social Security organization, Medicare and investment were prioritized. The results made the gap clear and paved the way for performance-based budgeting.