We use a stochastic frontier analysis (SFA) model to investigate the impact of domestic and foreign R&D on agricultural productivity for a sample of 30 sub-Sahara African (SSA) countries during the period 1981–2011. The results reveal that total factor productivity is strongly influenced by both domestic and foreign R&D spending in the agricultural sector, albeit the former plays a more important role. The decomposition of total factor productivity (TFP) and its components show an annual average rate of productivity growth of 4.8%, driven mainly by technical change which had an average annual improvement of 3.2%. Efficiency change had a negative impact on productivity and generally exhibited a net reduction in TFP growth at an average annual growth rate of −0.8%. Our sub-regional analyses indicate the West African region recorded the highest productivity growth during the period under consideration. Overall, our findings highlight the crucial role of knowledge stocks in driving agricultural productivity in the SSA region.