The calibration of 3D cameras is one of the key challenges to successfully measure the nightly 3D flight tracks of bats with thermal cameras. This is relevant around wind turbines to investigate the impact wind farms have on their species. Existing 3D-calibration methods solve the problem of unknown camera position and orientation by using a reference object of known coordinates. While these methods work well for small monitoring volumes, the size of the reference objects (e.g., checkerboard patterns) limits the distance between the two cameras and therefore leads to increased calibration errors when used in large outdoor environments. To address this limitation, we propose a calibration method for tracking flying animals with thermal cameras based on UAV GPS tracks. The tracks can be scaled to the required monitoring volume and accommodate large distances between cameras, which is essential for low-resolution thermal camera setups. We tested our method at two wind farms, conducting 19 manual calibration flights with a consumer UAV, distributing GPS points from 30 to 260 m from the camera system. Using two thermal cameras with a resolution of 640 × 480 pixels and an inter-axial distance of 15 m, we achieved median 3D errors between 0.9 and 3.8 m across different flights. Our method offers the advantage of directly providing GPS coordinates and requires only two UAV flights for cross-validation of the 3D errors.