Compact and efficient 6DoF object pose estimation is crucial in applications such as robotics, augmented reality, and space autonomous navigation systems, where lightweight models are critical for real-time accurate performance. This paper introduces a novel uncertainty-aware end-to-end Knowledge Distillation (KD) framework focused on keypoint-based 6DoF pose estimation. Keypoints predicted by a large teacher model exhibit varying levels of uncertainty that can be exploited within the distillation process to enhance the accuracy of the student model while ensuring its compactness. To this end, we propose a distillation strategy that aligns the student and teacher predictions by adjusting the knowledge transfer based on the uncertainty associated with each teacher keypoint prediction. Additionally, the proposed KD leverages this uncertainty-aware alignment of keypoints to transfer the knowledge at key locations of their respective feature maps. Experiments on the widely-used LINEMOD benchmark demonstrate the effectiveness of our method, achieving superior 6DoF object pose estimation with lightweight models compared to state-of-the-art approaches. Further validation on the SPEED+ dataset for spacecraft pose estimation highlights the robustness of our approach under diverse 6DoF pose estimation scenarios.