The purpose of this study is to explore reasons for the decline in agricultural performance in Botswana that has occurred during the implementation of a variety of policy measures, as well as the introduction of new technologies, and to identify ways in which it might be reversed. Panel data from six regions in Botswana (period 1979-2012) is analyzed with a stochastic output distance function and inefficiency effects model. We decompose agricultural output growth into; total factor productivity (TFP) and changes in input use (factors of production). TFP is further decomposed into scale effects, technical efficiency and technological change. The results show that over the study period agricultural output grew at a very low rate of 0.072 percent per year, which is largely due to a growth in factors of production at 0.071 percent per year rather than TFP growth (which declined at 0.003 percent per year). We found that the decline in productivity has been due to technological regress and low growth in technical efficiency and scale efficiency. Policy options aimed at improving agricultural productivity and output growth will require the strengthening of extension services; improving the agronomic and husbandry management skills of farmers through training; and by encouraging farmers to adopt and utilize technologies that have been provided under existing policy programs.