The use of ground control points (GCPs) for georeferencing is the most common strategy in unmanned aerial vehicle (UAV) photogrammetry, but at the same time their collection represents the most time-consuming and expensive part of UAV campaigns. Recently, deep learning has been rapidly developed in the field of small object detection. In this letter, to automatically extract coordinates information of ground control points (GCPs) by detecting GCP-markers in UAV images, we propose a solution that uses a deep learning-based architecture, YOLOv5-OBB, combined with a confidence threshold filtering algorithm and an optimal ranking algorithm. We applied our proposed method to a dataset collected by DJI Phantom 4 Pro drone and obtained good detection performance with the mean Average Precision (AP) of 0.832 and the highest AP of 0.982 for the cross-type GCP-markers. The proposed method can be a promising tool for future implementation of the end-to-end aerial triangulation process.