In arid and semi-arid climates, Balanites aegyptiaca (B. aegyptiaca) is a potential plant to produce oilseed-based biofuels. In this paper an optimization model for a wild biomass supply chain is presented. The model was developed to identify the optimal organization of the supply network that minimizes the cost of supplying the feedstock. It was applied to a case study on a B. aegyptiaca seed supply chain in Burkina Faso. Considering different means of transport and different pre-processing locations, the results show that in contexts such as Burkina Faso’s, the most efficient option for the supply of B. aegyptiaca seeds is using animal drawn carts to transport the biomass from the harvest sites to the collection points. Feedstock pre-processing should take place before transport and an improvement in pre-processing operations by mechanical de-hulling could help reduce the cost price of the seeds. The results also show that more than 35% of the cost price of B. aegyptiaca seed is accounted for by transport costs. Pre-processing, handling, and storage costs account for about 50% of the cost of the seeds.