Over the past years, transparency has been the focus of policy makers and academic circles as one of the characteristics of good governance and a mechanism for the balance of power between the government and the people. Transparency in the activities and decision-making process of government institutions can prevent financial scandals, poor decision-making, lack of accountability, and ineffective governance of these institutions. There is also a need to pursue and implement transparency in the organizations involved in the science and technology system that use public budgets. One of the most important organizations in the science and technology system are research funding organizations. Transparency in these organizations is essential because they use public budgets and play a fundamental role in the distribution of financial resources. Moreover, the lack of transparency in these organizations will not only increase financial violations and corruption, but will also affect the country’s research and development path in the long run. The review of previous research shows that the dimensions of information that need to be clarified in research funding organizations and the priority of these dimensions in clarification are not clear, and there is a research gap in this field. Considering the importance of the issue, this article intends to know the different dimensions of transparency in research funding organizations and their prioritization. In this regard, by reviewing scientific literature and conducting semi-structured and structured interviews with experts, the dimensions of information that should be clarified in research funding organizations have been identified. Then, we examine the websites of two research funding organizations in Iran (Supreme Council of Science, Research and Technology (ATF) and Iran National Science Foundation) in terms of transparency in these dimensions. The identified dimensions are 11 items including regulations and guidelines for financing, opinions of judges and examiners of proposals, research data used in the project, and output of projects receiving financial assistance. The results show that many dimensions of transparency have not been taken into account in these two organizations and it is necessary for these organizations to put transparency on their agenda.