The durability challenge of fuel cell technology is one of the main obstacles that hinder its wide commercialization. This work proposes a post-prognostics decision-making strategy to manage the economic lifetime of a two-stack PEMFC system. The influence of fuel cell deterioration and fuel consumption on fuel cell economic lifetime is studied. These two items are combined to construct the mixed decision criterion. Both the constant and dynamic type of system load demand are tested by the decision-making strategy. In simulation work, the hydrogen consumption/system-lifetime ratio and system lifetime are proposed as two evaluation criteria to assess the efficiency of the proposed decisionmaking strategy. Both the constant load and dynamic load simulation results show that when more weight is put on mitigating fuel cell deterioration, a bigger hydrogen consumption/system-lifetime ratio is achieved. For the system lifetime, an obvious increasing trend is observed when putting more weight on mitigating fuel cell deterioration. The proposed strategy can adequately handle the two items in the mixed criterion, generating the optimal load repartition for two-stack fuel cell systems. Therefore, a better economic lifetime can be achieved for the two stacks fuel cell system.