An advanced biofuels supply chain is proposed to reduce biomass transportation costs and take advantage of the economics of scale for a gasification facility. In this supply chain, biomass is converted to bio-oil at widely distributed small-scale fast pyrolysis plants, and after bio-oil gasification, the syngas is upgraded to transportation fuels at a centralized biorefinery. A two-stage stochastic programming is formulated to maximize biofuel producers' annual profit considering uncertainties in the supply chain for this pathway. The first stage makes the capital investment decisions including the locations and capacities of the decentralized fast pyrolysis plants as well as the centralized biorefinery, while the second stage determines the biomass and biofuels flows. A case study based on Iowa in the U.S. illustrates that it is economically feasible to meet desired demand using corn stover as the biomass feedstock. The results show that the locations of fast pyrolysis plants are sensitive to uncertainties while the capacity levels are insensitive. The stochastic model outperforms the deterministic model in the stochastic environment, especially when there is insufficient biomass. Also, farmers' participation can have a significant impact on the profitability and robustness of this supply chain.