In this paper, a Passive Fault Tolerant Control strategy dedicated to air feeding system fault based on an auto-tuning PID regulator is designed and implemented on a real fuel cell test bench. The present work compares the auto-tuning PID strategy performance to classical PID controller and highlights its benefits during faulty operation. Experimental results demonstrate the effectiveness of the proposed approach to regulate oxygen stoichiometry in real-time operation while maintaining a proper system performance under faulty situations. Unlike the classical PID controller, the proposed Passive Fault Tolerant Control System shows highly satisfactory performance in terms of setpoint tracking accuracy and disturbances rejection capability during faulty operations.