The effectiveness of a national innovation system can create numerous opportunities; however, these systems may become inefficient due to various factors, leading to what is known as systemic failure. Consequently, this study aims to analyze the systemic failures within Iran's national innovation system. By recognizing the interdependence of structures and functions in innovation systems, a combined structural-functional approach was employed for this analysis. The research framework was developed through documentary analysis, identifying four structural elements and twelve functional factors. Additionally, the systemic failures of Iran's national innovation system were assessed based on insights from 89 science and technology policy experts, gathered through ten focus groups. The findings indicate that the most significant weakness in Iran's innovation system lies within the structural element of institutions, with the greatest failures occurring in the functions related to institutionalization. Therefore, it is strongly recommended that institutional structures be enhanced and that both soft and hard institutions be established to address the systemic failures faced by Iran's innovation system.