Biomass can be converted to transportation fuels through gasification. However, commercialization of biomass gasification has been hampered by its high capital and operating costs, in addition to the difficulties of transporting bulky solid biomass over a long distance. A novel approach is to convert biomass to bio-oil at widely distributed small-scale fast pyrolysis plants, transport the bio-oil to a centralized location, gasify the bio-oil to syngas, and upgrade the syngas to transportation fuels. In this paper, a two-stage stochastic programming is formulated. The first-stage makes the capital investment decisions including the locations and capacities of the bio-facilities (fast pyrolysis and refining facility) while the second-stage determines the biomass and biofuels flows. This paper aims to find the optimal design of the supply chain for this certain path considering uncertainties in biomass yield, biofuel price and transportation costs.