Batteries are a key enabling technology for the decarbonization of transport and energy sectors. The safe and reliable operation of batteries is crucial for battery-powered systems. In this direction, the development of accurate and robust battery state-of-health prognostics models can unlock the potential of autonomous systems for complex, remote and reliable operations. The combination of Neural Networks, Bayesian modelling concepts and ensemble learning strategies, form a valuable prognostics framework to combine uncertainty in a robust and accurate manner. Accordingly, this paper introduces a Bayesian ensemble learning approach to predict the capacity depletion of lithium-ion batteries. The approach accurately predicts the capacity fade and quantifies the uncertainty associated with battery design and degradation processes. The proposed Bayesian ensemble methodology employs a stacking technique, integrating multiple Bayesian neural networks (BNNs) as base learners, which have been trained on data diversity. The proposed method has been validated using a battery aging dataset collected by the NASA Ames Prognostics Center of Excellence. Obtained results demonstrate the improved accuracy and robustness of the proposed probabilistic fusion approach with respect to (i) a pseudo-Bayesian model averaging, (ii) a pseudo-Bayesian model averaging with Bayesian bootstrapping, and (iii) a point prediction stacking strategy based on different BNNs.