This paper provides insight into Uganda’s evolving innovation system. The framework used to gain this insight presents science, technology and innovation as a function of financing, governance, human capital and the strength of interactions within and across the functional spheres. From the framework, it appears universities and public research organizations are playing a major role in building Uganda’s innovation system. Public research organizations should, however, collaborate more closely with universities, and be more pragmatic in technology dissemination. It seems that in Uganda the public sector will continue to play a leading role in fostering innovation in the foreseeable future as the private sector grows. A crucial element of the public sector support is to have in place stable merit-based system of science funding where competitive grants are awarded annually for research and innovation.