Learning-based navigation systems are widely used in autonomous applications, such as robotics, unmanned vehicles and drones. Specialized hardware accelerators have been proposed for highperformance and energy-efficiency for such navigational tasks. However, transient and permanent faults are increasing in hardware systems and can catastrophically violate tasks safety. Meanwhile, traditional redundancy-based protection methods are challenging to deploy on resource-constrained edge applications. In this paper, we experimentally evaluate the resilience of navigation systems with respect to algorithms, fault models and data types from both RL training and inference. We further propose two efficient fault mitigation techniques that achieve 2× success rate and 39% qualityof-flight improvement in learning-based navigation systems.