Neural signals are typical nonstationary data where the functional mapping between neural activities and the intentions (such as the velocity of movements) can occasionally change. Existing studies mostly use a fixed neural decoder, thus suffering from an unstable performance given neural functional changes. We propose a novel evolutionary ensemble framework (EvoEnsemble) to dynamically cope with changes in neural signals by evolving the decoder model accordingly. EvoEnsemble integrates evolutionary computation algorithms in a Bayesian framework where the fitness of models can be sequentially computed with their likelihoods according to the incoming data at each time slot, which enables online tracking of time-varying functions. Two strategies of evolve-at-changes and history-model-archive are designed to further improve efficiency and stability. Experiments with simulations and neural signals demonstrate that EvoEnsemble can track the changes in functions effectively thus improving the accuracy and robustness of neural decoding. The improvement is most significant in neural signals with functional changes.