This paper describes the synthesis of a rubber seed supply network to support the green energy demand in Malaysia. An optimised rubber seed supply network design, which maximises biomass utilisation, secures local biomass supply as well as reduces material loss and emissions resulted from inefficient logistic activities has been carried out. The utilisation of rubber seed oil (RSO) for biofuel production in Malaysia and its contribution to the national biomass renewable energy portion is forecasted. The supply network of the biomass is synthesised through mixed integer linear programming. Both centralised and de-centralised rubber seed processing facilities are studied. The network model shows that the selection of rubber seed processing plant is highly dependant on the volume of feedstock. A simplified real case study is presented to demonstrate the optimisation model. In addition, biodiesel price is largely dependent on the feedstock market. Thus, comparison of crude palm oil (CPO) and RSO production processes have been made in term of (i) energy and utility consumptions, (ii) feedstock price and (iii) environmental impact. Sensitivity analysis of rubber seed oil price for obtaining optimal blending ratio of rubber seed oil and crude palm oil has been performed in order to determine the market uncertainty of the biodiesel price. The potential of substituting rubber seed oil for crude palm oil as an alternative blending feedstock for biodiesel production has been validated. © 2013 Elsevier Ltd.