Reliability of proton exchange membrane fuel cells (PEMFCs) is a major issue for large industrialization and commercialization. Indeed, performance can be degraded due to abnormal operating conditions, namely, faults, which lead either to a transient decay of the fuel cell performance or to permanent damage that cannot be recovered. The literature shows that long-time exposure to faults leads to fuel cell degradation. Therefore, it is necessary to use tools that can not only diagnose these faulty conditions, but also modify the fuel cell operations to recover a healthy operating point. For that purpose, one approach is the Active Fault Tolerant Control (AFTC) strategy which is composed of three functions. First, a diagnosis part allows fault detection and identification. Then a decision part, which is an algorithm aiming at finding a new operating point that mitigates the occurring fault. Finally, a control part applies the mitigation strategy established by the decision algorithm. The present work focuses on the decision part. and aims to bring a new contribution to PEMFCs reliability improvement and address water management issues, namely, the cell flooding and membrane drying out with the developed AFTC tool. The strategy is tested and validated on a single PEMFC cell and results are presented, analyzed, and discussed.