Accurate path following is challenging for autonomous robots operating in uncertain environments. Adaptive and predictive control strategies are crucial for a nonlinear robotic system to achieve high-performance path following control. In this paper, we propose a novel learning-based predictive control scheme that couples a high-level model predictive path following controller (MPFC) with a low-level learning-based feedback linearization controller (LB-FBLC) for nonlinear systems under uncertain disturbances. The low-level LB-FBLC utilizes Gaussian Processes to learn the uncertain environmental disturbances online and tracks the reference state accurately with a probabilistic stability guarantee. Meanwhile, the high-level MPFC exploits the linearized system model augmented with a virtual linear path dynamics model to optimize the evolution of path reference targets, and provides the reference states and controls for the low-level LB-FBLC. Simulation results illustrate the effectiveness of the proposed control strategy on a quadrotor path following task under unknown wind disturbances.