This paper presents the first stochastic mixed integer programming model for a comprehensive hybrid power system design, including renewable energy generation, storage device, transmission network, and thermal generators, in remote areas. Given the computational complexity of the model, we developed a Benders’ decomposition algorithm with Pareto-optimal cuts. Computational results show significant improvement in our ability to solve this type of problem in comparison to a state-of-the-art professional solver. This model and the solution algorithm provide an analytical decision support tool for the hybrid power system design problem.