The remaining useful life (RUL) prediction for hydrogen fuel cells is an important part of its prognostics and health management (PHM). Artificial neural networks (ANNs) are proven to be very effective in RUL prediction, as they do not need to understand the failure mechanisms behind hydrogen fuel cells. A novel RUL prediction method for hydrogen fuel cells based on the gated recurrent unit ANN is proposed in this paper. Firstly, the data were preprocessed to remove outliers and noises. Secondly, the performance of different neural networks is compared, including the back propagation neural network (BPNN), the long short-term memory (LSTM) network and the gated recurrent unit (GRU) network. According to our proposed method based on GRU, the root mean square error was 0.0026, the mean absolute percentage error was 0.0038 and the coefficient of determination was 0.9891 for the data from the challenge datasets provided by FCLAB Research Federation, when the prediction starting point was 650 h. Compared with the other RUL prediction methods based on the BPNN and the LSTM, our prediction method is better in both prediction accuracy and convergence rate.