The shortage of qualified health professionals is a major obstacle to achieving better health outcomes in many parts of the world, particularly in Africa. The role of health science universities in addressing this shortage is to provide quality education and continuing professional development opportunities for the healthcare workforce. Academic institutions in Africa, however, are also short of faculty and especially under-resourced. We describe the initial phase of an institutional partnership between the Muhimbili University of Health and Allied Sciences (MUHAS) and the University of California San Francisco (UCSF) centred on promoting medical education at MUHAS. The challenges facing the development of the partnership include the need: (1) for new funding mechanisms to provide long-term support for institutional partnerships, and (2) for institutional change at UCSF and MUHAS to recognize and support faculty activities that are important to the partnership. The growing interest in global health worldwide offers opportunities to explore new academic partnerships. It is important that their development and implementation be documented and evaluated as well as for lessons to be shared.