In this paper, a Fault Tolerant Control Strategy (FTCS) dedicated to PEMFC (Polymer Electrolyte Membrane Fuel Cell) water management is implemented and validated online on a real PEMFC system. Thanks to coupling a Fault Detection and Isolation (FDI), an adjustable controller and a reconfiguration mechanism, FTCS allows addressing the important challenge of Fuel Cell (FC) reliability improvement. Only few works have already been conducted on FTCS applied to FC actuators faults, and none of them on FC water management faults. In this work, a neural-based diagnosis tool is computed online as FDI component and is coupled to a self-tuning PID controller. This diagnosis tool shows low computational time and high detection performance. The self-tuning PID controller shows robustness against noise measurements and model uncertainties. Its low computational cost makes it a suitable control method for real-time FTCS. Performed on a PEMFC system, the FTCS shows promising results on fault diagnosis and performance recovery.