To participate fully in the global knowledge economy, all countries require strong research and innovation eco-systems. This crucially depends on the efficiency of doctoral education and training. We examined the trajectory of doctoral education in Uganda over the past four decades focusing on number of doctoral awards and equity in regard to sex, STEM versus Arts, Humanities and Social Sciences, and private versus public providers. We collected data from all institutions providing doctoral education in Uganda through comprehensive review of documents. Our analysis of data revealed low capacity for doctoral education in Uganda. There was under production of doctorates depicted by the low number of doctoral awards; and inequalities in regard to sex, STEM versus Arts, Humanities and Social Sciences, and the public versus private providers. We argue that the trends in equity and number of doctoral awards translate into low number of researchers per million inhabitants, low number of researchers engaged in research and development (R&D), and gender disparity in researchers' participation in R&D. We conclude that the low number and inequalities in doctoral awards have deterring implications to the attainment of national development goals. We proffer desired trajectories for the future of doctoral education and training in Uganda.