Background and purpose: The cost of health care has an increasing trend worldwide. Therefore, governments aim at analyzing the economic aspects of health services and make interventions in improving the financial performance of health care systems. This study was conducted to assess the new financial system of medical universities in Iran using SWOT analysis.

Materials and methods: This cross sectional study was done in 2013. The study population included the financial managers and experts in Iran’s health system. They were selected by census sampling and the Board of Health Budget Committee including 20 people were recruited. In order to assess the viewpoints of participants, strategic planning model was investigated using the SWOT matrix [strengths, weakness (internal factors), opportunities, and threats (external factors)]. Analytical hierarchy process was applied to weight and prioritize the items.

Results: Four items in strengths, 15 in weakness, 7 in opportunities and 6 items in threats were extracted by the committee members. The score for internal factors (strengths and weakness) in SWOT table was 1.98 and the score for external factors (opportunities and threats) was 4.23.

Conclusion: According to the results, external factors were found to have more effect on shaping the financial system in health care services in Iran which indicates a powerful impact of external organizations. Therefore, permanent finance subcommittees should be formed for effective and constant communication with external bodies.