Based on rapeseed plantation biodiesel production system requires transportation of goods, like raw materials, machines and tools, and products between various conversion stages of agricultural as well as industrial subsystems. Each transportation step requires consumption of some energy. This consumption, decreases the net amount of energy delivered out of the biofuel production system, and consequently decreases energetic efficiency of the system. The present work deals with computer modelling of the influence of energy consumed on those transport routes on the energetic efficiency of production system. The effects caused by variation of several parameters like fuel consumption and load capacity of transportation means, size of plantation, distribution and sizes of individual fields, distances between fields, as well as plantation yield, and finally the distance between plantation and the industrial facility are studied using the numerical model developed