Although agricultural innovation systems (AIS) have recently received considerable attention in academic and development circles, links between an AIS's regional specifications and structural-functional analysis have been neglected. This paper aims to understand how regional and structural dimensions determine systemic problems and blocking mechanisms that, in turn, hinder a regional AIS's function. From the basis of a qualitative data set, it presents an analysis of an AIS in Vietnam's Northern Uplands using an integrated regional-structural-functional framework. Results indicate that the existing AIS has six unique problems that are linked to seven blocking mechanisms, mainly belonging to three structural components: infrastructure, actors and institutions. Addressing these blocking mechanisms needs systemic instruments that help stimulate and balance investments, creating spaces for the development of actors' capability, and facilitating the institutional shift towards enabling region-oriented agriculture and demand-driven innovation processes. First, this study contributes an analysis of the integration of regional dimensions and technologies captured as a structural entity into the structural-functional framework, providing novel insights into the functioning of a regional AIS. Second, it deepens the literature on structural-functional innovation systems analysis by looking at the interconnections between structural and regional dimensions and how they create blocking mechanisms. It concludes that the regional-structural-functional analysis allows the design of integrated coherent sets of systemic instruments for a regional AIS.