The transportation sector is a key pillar of Iran’s economy and an important factor in national competitiveness. However, dispersed innovation activities, weak institutional coordination, and the lack of an integrated governance mechanism have limited the commercialization of innovations. Although innovation management literature emphasizes transparent governance and structured interaction between public and private sectors, Iran lacks a clear framework for governing the transportation innovation ecosystem. This study adopts an institutional design approach based on the MIT innovation ecosystem framework. Potential roles and actors were identified through literature and policy document review, and the combination of governance institutions was determined using the Delphi method with experts. The results identified five key roles within a “Transportation Innovation Ecosystem Governance Council.” Three criteria were also proposed to guide innovative projects: market demand orientation, technology readiness level, and total cost of ownership advantage. The model aims to strengthen coordination and improve technology commercialization in Iran’s transportation sector.