This research focuses on the supply chain network design of a fast pyrolysis and hydroprocessing production pathway by utilizing corn stover as feedstock to produce gasoline and diesel fuel. A mixed integer linear programming (MILP) model was formulated to optimize fast pyrolysis and hydroprocessing facility locations and capacities to minimize total system cost, including the feedstock collecting costs, capital costs of facilities, and transportation costs. The economic feasibility of building a new biorefinery in Iowa was analyzed based on the optimal supply chain configuration and savings in bio-oil logistic costs to the centralized upgrading facility.