The prognostic of proton exchange membrane fuel cells (PEMFCs) degradation and the estimation of its remaining useful life (RUL) are effective ways to improve the reliability of the target system and reduce maintenance costs, which is of great significance for the wide commercialization of PEMFCs. Many factors cause the degradation of PEMFCs, and these factors are often difficult to measure accurately. The prognostic method based on long short-term memory networks (LSTMs) has better memory ability for time series and has been demonstrated able to describe the degradation trend of PEMFCs. However, the traditional LSTM prediction algorithm seems to easily fall into the local optimal solution in long-term prediction cases. Overfitting like errors may result in an imprecise or even unstable prognostic. This paper proposes a novel method, named navigation sequence driven LSTMs (NSD-LSTMs), to enhance the accuracy of PEMFCs degradation trend prediction. Two types of PEMFCs aging test data under different load conditions were used to verify the performance of NSD-LSTMs. Experimental results show that, compared with traditional LSTMs, NSD-LSTMs can improve the accuracy of trend prediction. Accurate degradation prognostic can be used to predict RUL and provide guidance for the commercial application of PEMFCs.