Biofuel energy as an alternative and additive form of energy to fossil fuel has gained much attention in recent times. In order to sustain such a vision, a robust supply chain is of extreme importance in helping to deliver competitive biofuel to the end user markets. In this paper, firstly, an introduction of the evolution of biofuels and the general structure of the biofuel supply chain are presented. Secondly, the three types of decision making levels and uncertainties that are inherent within the biofuel supply chain are discussed. Thirdly, important methodologies for modeling uncertainties in the decision making process are provided. Fourthly, sustainability concepts and models that give perspectives to the social, economical and environmental concepts are reviewed. Finally, conclusions and future research based on incorporating uncertainties and sustainability concepts within the biofuel supply chain are drawn and suggested, respectively.