Purpose: The rapidly evolving nature of agricultural innovation processes in low-income countries requires agricultural extension agencies to transform the classical roles that previously supported linear information dissemination and adoption of innovation. In Bangladesh, strengthening agricultural innovation calls for facilitation of interactive communication and a wide range of mediation tasks within (and between) stakeholders operating in different social spheres. This paper examines how a public-sector agricultural extension agency has attempted to change its roles in implementing a major agricultural extension project in order to strengthen agricultural innovation. This role adjustment is a key outcome of an effectively functioning innovation system because it enables collective actions and enhances performance that meets the needs of clients. Methodology: The study uses a case study design that includes mixed methods data collection and analysis. Using interviews, group discussions, observations, and a semi-structured survey, data were collected from stakeholders of a major regional agricultural extension project in Bangladesh. Findings: The findings suggest that the agricultural extension agency missed the opportunity to deliver the agricultural extension project in such a way that it strengthens collective actions and functions that would respond to the needs of all clients within the system. This is due to institutions that create obstacles within the agricultural innovation system. These obstacles relate to the tendency to remain in a linear paradigm of technology transfer and dependency on public service, the under-estimation and depreciation of intermediary roles of extension personnel (e.g. brokering, negotiating, convening), and finally, an inability to foresee extension methods (e.g. training, demonstration) as the facilitation of interactive learning and knowledge embedding processes. Originality/ Practical Implications: This is the first case study from Bangladesh that provides insights into extant initiatives taken by a public-sector agricultural extension agency to put innovation system thinking into use. The paper discusses a number of lessons, which will be useful for evolving new forms of extension work and applying agricultural innovation systems thinking in low-income countries.