<jats:title>Abstract</jats:title><jats:p>Kusatsu-Shirane volcano is one of the active volcanoes in Japan. Phreatic explosions occurred in Mt. Shirane in 1983 and most recently, in 2018, in Mt. Motoshirane. Information on the subsurface structure is crucial for understanding the activity of volcanoes with well-developed hydrothermal systems where phreatic eruptions occur. Here, we report aeromagnetic surveys conducted at low altitudes using an unmanned helicopter. The survey aimed to obtain magnetic data at a high spatial resolution to map the magnetic anomaly and infer the magnetization intensity distribution in the region immediately after the 2018 Mt. Motoshirane eruption. The helicopter used in the survey was YAMAHA FAZER R G2, an autonomously driven model which can fly along a precisely programmed course. The flight height above the ground and a measurement line spacing were set to ~ 150 m and ~ 100 m, respectively, and the total flight distance was 191 km. The measured geomagnetic total intensity was found to vary by ~ 1000 nT peak-to-peak. The estimated magnetization intensity derived from measured data showed a 100 m thick magnetized surface layer with normal polarity, composed of volcanic deposits of recent activities. Underneath, a reverse-polarity magnetization was found, probably corresponding to the Takai lava flow in the Early Quaternary period (~ 1 Ma) mapped in the region. Our results demonstrate the cost-effectiveness and accuracy of using drone magnetometers for mapping the rugged terrain of volcanoes.</jats:p>