The partial feedback linearizing controller design approach is presented in this paper, for a proton exchange membrane fuel-cell (PEMFC)-based energy storage system. The PEMFC system is connected to the three-phase grid through a voltage source converter (VSC). The dynamical model of the PEMFC is developed from the electrical equivalent circuit, and then based on the developed model partial feedback linearizing controller is employed to regulate the active and reactive power injection from the PEMFC system to the three-phase grid supply point. The dq-axes components of the grid current corresponding to the active and reactive power are controlled to accomplish the control objective. The partial feedback linearizing controller is implemented after investigating stability of the internal dynamics of grid-connected PEMFC system, as stable internal dynamics are crucial for the implementation of this type of controller. Third harmonic injected (THI) modulation scheme is incorporated with the partial feedback linearizing controller to increase efficiency of the controller. Finally, the performance of the proposed control approach is validated through simulation results under different grid events in a three-phase grid-connected PEMFC system, and in the CIGRE low voltage distribution network.