Limited access to energy has led to interest in biofuels in most West African countries where Jatropha curcas (jatropha) has been the most widely studied energy crop. However, due to difficulties in obtaining enough jatropha seed at acceptable costs, Balanites aegyptiaca (B. aegyptiaca) could be an alternative feedstock for biofuel production at lower costs. We report the results of a comparative study of the optimal supply cost and supply network configuration of a cultivated and a wild energy crop. These optimal items were determined using a mixed integer linear programming model designed to help decision making concerning biomass supply chains for biofuel production. The model was applied to a case study on jatropha and B. aegyptiaca seed supply chains in Burkina Faso. By considering different options for location and technologies used for pre-processing as well as different cropping systems for jatropha cultivation, the case study showed that in contexts like those found in Burkina Faso, a wild energy crop like B. aegyptiaca cannot be competitive compared to cultivated energy crops like jatropha because of its costly logistic operations.