This paper presents a UAV based remote sensing system for the detection of fawns in the meadows. There is a high demand because during pasture mowing many wild animals, especially roe deer fawns are killed by mowing machines. The system was tested in several real situations especially with differing weather and iluminating conditions. Its primary sensor is a lightweight thermal infrared camera. The images are captured onboard of the flight system and also transmitted as analog video stream to the ground station, where the user can follow the camera live stream on a monitor for manual animal detection. Beside a high detection rate a fast workflow is another very important objective for this application. Therefore a waypoint planning software was developed that accelerates the workflow. At adequate illuminating and weather conditions the presented UAV-based fawn detection via thermal imaging is a comfortable, fast and reliable method.