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This paper presents a synergetic controller for pulse current charging of advanced batteries from a fuel cell power source. Pulse current charging protocol that has been shown to have many advantages over the traditional constant current/constant voltage protocol is applied in a fuel cell powered battery-charging station to reduce the total charging time. Strong nonlinearity and dynamics exist in such systems. In this paper, the synergetic control approach is applied to regulate the buck converters that control the pulse charging currents to the many batteries. A practical synergetic controller to coordinate pulse current charging of the battery is synthesized and discussed. It provides asymptotic stability with respect to the required operating modes, invariance to load variations, and robustness to variation of the input and converter parameters. The synergetic controller is then implemented in Simulink. The dynamic characteristics of the synergetic controller are studied and compared with PI controller by conducting system simulation and experimental tests. Simulation and experiment results show the synergetic controller is robust for such nonlinear dynamic system and achieves better performance than the standard PI controller.