A well-articulated institutional health research agenda can assist essential contributors and intended beneficiaries to visualize the link between research and community health needs, systems outcomes, and national development. In 2011, Tanzania's Muhimbili University of Health and Allied Sciences (MUHAS) published a university-wide research agenda. In developing the agenda, MUHAS leadership drew on research expertise in its five health professional schools and two institutes, its own research relevant documents, national development priorities, and published literature. We describe the process the university underwent to form the agenda and present its content. We assess MUHAS's research strengths and targets for new development by analyzing faculty publications over a five-year period before setting the agenda. We discuss implementation challenges and lessons for improving the process when updating the agenda. We intend that our description of this agenda-setting process will be useful to other institutions embarking on similar efforts to align research activities and funding with national priorities to improve health and development.