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Nonlinear model predictive control (MPC) is a flexible and increasingly popular framework used to synthesize feedback control strategies that can satisfy both state and control input constraints. In this framework, an optimization problem, subjected to a set of dynamics constraints characterized by a nonlinear dynamics model, is solved at each time step. Despite its versatility, the performance of nonlinear MPC often depends on the accuracy of the dynamics model. In this work, we leverage deep learning tools, namely knowledge-based neural ordinary differential equations (KNODE) and deep ensembles, to improve the prediction accuracy of this model. In particular, we learn an ensemble of KNODE models, which we refer to as the KNODE ensemble, to obtain an accurate prediction of the true system dynamics. This learned model is then integrated into a novel learning-enhanced nonlinear MPC framework. We provide sufficient conditions that guarantees asymptotic stability of the closed-loop system and show that these conditions can be implemented in practice. We show that the KNODE ensemble provides more accurate predictions and illustrate the efficacy and closed-loop performance of the proposed nonlinear MPC framework using two case studies.