Innovation systems consist of a set of players and institutions that work to obtain specific functions. Structures and functions have interactive effects on each other and it is not possible to separately study them in a systemic and comprehensive manner. Structures, will shape functions and functions condition structures accordingly. Furthermore, innovation systems are frequently, facing possible challenges and failures. These failures could be classified into three general categories; Structural failures, Market failure and System transition failure. The purpose of this study is to present a comprehensive and systemic analysis on Iran’s sectoral innovation of medicinal and aromatic plants (MAP) system. We used a three-folded functional- structural-transitional conceptual framework to analyze MAP innovation system . In this case study research we collected data from different sources including public and archival data, interviews, direct research and participant observation. Results show that the Iran’s medicinal and aromatic plants sector has multiple structural failures that is unable to shape the desired functions expected from an innovation system. We present, some policy recommendations to overcome the sector challenges.