Current research on prognostics of PEMFC mainly focuses on one stack. However, in practice, the PEMFC stacks are assembled together to provide higher and more reliable power. In this paper, an original multiagent approach is proposed for predicting the remaining useful life‐times of all stacks in a multistack PEMFC system. The predictions are updated dynamically by particle filtering when new stack loads are collected. The major contribution of the paper is not on degradation modeling of a single PEMFC, but on the cooperative prognostics of multiple PEMFC stacks in the same power system. A case study concerning a synthetic combined heat and power system with three PEMFC stacks is considered and the results show the effectiveness of the proposed approach.