The use of proton exchange membrane fuel cells (PEMFC) presents many advantages in stationary and embedded systems. Their operating conditions and load profile as well as efficiency and lifetime are highly dependent on the type of application. Indeed, stationary installations are easier to maintain at an optimal operating point, as the dynamics are slow and the load profile presents large constant phases. Embedded ones are exposed to more constraints, such as fast-dynamics' user profile, mechanical and thermal solicitations. This makes the optimal operating point more difficult to maintain. Furthermore, faults can appear and provoke a dramatic reduction of the lifespan of fuel cells. This fault occurrence depends on several factors such as the quality of inlet gases, their humidity, temperature, etc [1]. Therefore, finding the best compromise between efficiency and reliability of fuel cell systems is still an open issue to study. The Active fault tolerant control (AFTC) is one of the possible approaches to address this issue. It consists of associating diagnosis with control tools to mitigate fault. Only few papers have been written so far about this subject. This paper proposes an active fault tolerant control strategy to mitigate the most recurrent faults in PEMFC systems.