This paper develops a hierarchical reinforcement learning architecture for multi-mission spaceflight campaign design under uncertainty, including vehicle design, infrastructure deployment planning, and space transportation scheduling. This problem involves a high-dimensional design space and is challenging especially with uncertainty present. To tackle this challenge, the developed framework has a hierarchical structure with reinforcement learning (RL) and network-based mixed-integer linear programming (MILP), where the former optimizes campaign-level decisions (e.g., design of the vehicle used throughout the campaign, destination demand assigned to each mission in the campaign), whereas the latter optimizes the detailed mission-level decisions (e.g., when to launch what from where to where). The framework is applied to a set of human lunar exploration campaign scenarios with uncertain in-situ resource utilization (ISRU) performance as a case study. The main value of this work is its integration of the rapidly growing RL research and the existing MILP-based space logistics methods through a hierarchical framework to handle the otherwise intractable complexity of space mission design under uncertainty. We expect this unique framework to be a critical steppingstone for the emerging research direction of artificial intelligence for space mission design.