Unmanned aerial vehicle (UAV)‐based magnetometer systems became more and more attractive for large‐scale archaeological prospection in recent years. Although their sensors exhibit the same sensitivity than the ground‐based prospecting systems, UAV prospecting is seriously handicapped by the magnetic and mechanical disturbances of the drone and by limitations of a low‐level flight. To minimize these disturbances, scalar magnetometers are attached only on a tether 2.5–10 m beneath the drone to be flown as close as possible above the ground. First, test measurements with UAV‐fixed fluxgate magnetometers provide more accurate results than the scalar magnetometers in any configuration but have to overcome disturbance by vibrations. Here, we present a case study choosing the compact set‐up of the Sensys MagDrone R4. The high sampling rate of 200 Hz of the three axis fluxgate sensors of the R4 allows sufficient filtering of the interferences generated by the UAV and external disturbances. High‐precision flight control of the drone allows operating the sensors by radar‐controlled flight height ∼1 m above the ground, which is a fundamental and indispensable prerequisite for archaeological prospecting. For our test, we choose the site Ganacker (southern Bavaria), where we expected a large range of archaeological structures and features with high magnetic contrast. We compare and verify the magnetogram with historical and recent geodata. Our results show that the R4 system offers an outstanding step forward regarding a successful application for archaeological prospection. Already now, the system is well suited for the fast mapping of large areas and archaeological sites with intense magnetic anomalies.