The portable fuel-cell powered battery charging station provides a good solution to recharging batteries in field applications. This paper presents the design and testing of control strategies for this system using the Virtual Test Bed (VTB). The VTB provides a unique environment to model interdisciplinary components, to rapidly prototype the control system, and to simulate complex systems. In this paper, the system design is first proposed. Both static and real-time control strategies are investigated to coordinate the power distribution among batteries. The fuel cell, battery and power electronic system are modeled in the native VTB format. The charging controller is designed and implemented in MatLab/Simulink, and then is imported to VTB for system simulation. The fuel-cell powered battery charging station is simulated under the proposed charging algorithms. The performance of each charging algorithm is analyzed.