This study aims to design an optimal organizational structure for the establishment of the Supreme Council of Science, Research, and Technology Fund in Iran. Research and development (R&D) are pivotal in advancing national capacities and fostering economic resilience. In Iran, despite various financial resources, the fragmented funding allocation to research has been a significant challenge. Establishing a specialized fund aims to centralize financial support for research and innovation, aligning with national science and technology policies. The Supreme Council of Science, Research, and Technology Fund was proposed to address inefficiencies in Iran's decentralized research funding system. The fund's primary goal is to pool scattered resources across various governmental bodies and direct them toward national priorities in science and technology. To ensure the success of this fund, a comprehensive organizational structure is essential. This study reviews the legal frameworks, budgetary structures, and existing research funds to propose a model that optimizes resource allocation and management. Through detailed analysis, this paper proposes a new organizational chart, governance policies, and administrative guidelines for the fund. The goal is to establish a fund that operates efficiently, remains adaptable to evolving national needs, and encourages collaboration between academic institutions, industries, and government sectors. This study offers a blueprint for the strategic implementation of this fund, emphasizing transparency, accountability, and alignment with Iran’s long-term scientific and technological development goals.