Effective design of biodiesel supply chain network can reduce many of its high production costs. There are various uncertain parameters in real world that if ignored may greatly affect the optimal configuration of the designed biodiesel supply chain. Scenario planning is a powerful tool which can help the decision makers for long-term planning under uncertainties. Therefore, in this paper, a scenario-based robust optimization model is presented for designing the biodiesel supply chain networks under uncertainties. Some of the parameters including demand, supply, costs, and environmental impacts have uncertain nature. For the first time, in this study, the values of these uncertain parameters are estimated by a proposed scenario-planning method. The presented scenario-planning approach is based on cross-impact analysis and visualization methods. Non-edible sources such as Jatropha, Norouzak, and waste cooking oil are considered as raw materials of biodiesel production, and for the first time Norouzak has been used as one of the sources in designing biodiesel supply chain. In addition, an environmental constraint is considered and the environmental impacts of all processes are obtained by Eco-indicator 99 method. The presented model can determine the number, location, and capacity of the facilities. The proposed model is implemented in a real case study in Iran for a 7-year planning horizon. The results show the effectiveness of the presented approach in designing the biodiesel supply chain networks under uncertainties.