<p>Accurate dynamic models play a central role in achieving reliable control of quadcopters. Classical system identification methods remain widely used, mainly because of their interpretability. However, they often fail to capture important nonlinear effects, especially in small-scale aerial platforms where such effects become more pronounced. Data-driven approaches offer a different perspective. They can represent complex nonlinear dynamics more effectively, but this comes at the cost of reduced interpretability and the absence of well-calibrated uncertainty estimates. In this work, we propose a framework that combines physics-based modeling with data-driven learning, while explicitly accounting for uncertainty. A physics-based model is first identified using the Prediction Error Method (PEM), which captures the main structure of the system. The remaining dynamics are then modeled using a Gaussian Process (GP), allowing the residual behavior to be learned directly from data. This separation makes it possible to distinguish between known physical effects and unmodeled dynamics. The proposed framework is validated on a Duckiedrone-like experimental setup. The results show that the PEM–GP model achieves prediction accuracy comparable to that of a Long Short-Term Memory (LSTM) network, while additionally providing calibrated uncertainty estimates. This combination improves model reliability and supports uncertainty-aware decision-making.</p>