The higher education sector in Uganda has experienced tremendous improvements over the past two decades. It has also encountered numerous challenges that extend to the effects of massification on access, equity and quality. Through a review of existing literature and using international conventions and practices as benchmarks, this study gives an overview of the higher education sector in Uganda; it highlights productivity, production and utilisation of science, technology and innovations manifestations within the context of human capital development. With emphasis on agriculture education, the limitations discerned extend beyond scientific dependence and brain drain, to restrictions in scientific uptake and diffusion of new technologies across the value chain that have influenced the transition towards a knowledge based economy. The study concludes with prospects for an integrated system that will harness higher education as Africa engine for economic growth and development, whose relevance could apply across the sub- Saharan region.