The objective of this paper is to demonstrate a design optimization methodology for space transportation systems that integrates the vehicle design with the design of the flow through a transportation network. Traditionally, in the design of terrestrial transportation systems, each of these components or sub-systems has been analyzed and optimized separately and sequentially using previous design decisions as inputs. However, to define a system level architecture, it is advantageous to expand the system definition in the design process to include the vehicle specifications, network definitions, and the operations which couple the vehicles and the network. In this paper, the definition of a space transportation network is presented by extending modeling tools from operations research to incorporate the astrodynamic relationships of space transportation. The integrated transportation system model is then decomposed to define the models required for the vehicle definition, network flow, and operations. Utilizing the integrated transportation system formulation, the transportation architecture can be obtained by concurrently optimizing the vehicle design and network flow. This is accomplished by embedding an integer programming solver, CPLEX, in the perturbation step of Simulated Annealing to solve the large number of linear inequality and equality constraints imposed by the flow feasibility and operations constraints. The benefit of the methodology introduced in this paper is to enable the design of a space exploration logistics transportation system, where inefficiencies in the operations can be reduced during the design process.