Durability is considered as one of the main technical obstacles to the large-scale commercialization of proton exchange membrane fuel cells (PEMFCs), which can be effectively improved through degradation prediction techniques. This article proposes a stacked echo state network (ESN) based on the genetic algorithm (GA) to predict the future degradation trend of PEMFCs. By alternately using the projection layer and the encoding layer, the proposed method can make full use of the temporal kernel property of the ESN to encode the multiscale and multilevel dynamics of the stack voltage, thereby obtaining more robust generalization performance and higher accuracy than the existing methods. Specifically, a stack voltage time series of PEMFCs is projected into the high-dimensional echo state space of the reservoir. Then, an autoencoder projects the echo state representation into the low-dimensional feature space. After that, the GA is utilized to optimize the hyperparameters of the developed model. Based on two open-source datasets of PEMFCs with different accelerated test conditions, this article systematically tested the proposed degradation prediction methods based on different model structures. Test results demonstrate that the proposed method is superior to traditional prediction methods in terms of accuracy and generalization performance.