Unmanned aerial vehicles (UAVs) have recently drawn attention in various research fields for their ability to perform measurements, surveillance, and operations in hazardous areas. Our application is volcano surveillance, in which we used an unmanned autonomous helicopter to conduct a dense low-altitude aeromagnetic survey over Tarumae volcano, northern Japan.In autonomous flight, we demonstrated positioning control with an accuracy of approximately 10 m, which would be difficult for an ordinary crewed vehicle. In contrast to ground-based magnetic measurement, which is highly susceptible to local anomalies, the field gradient in the air with a terrain clearance of 100 to 300 m was fairly small at 1 nT/m. This result suggests that detection of temporal changes of an order of 10 nT may be feasible through a direct comparison of magnetic data between separate surveys by means of such a system, rather than that obtained by upward continuation to a common reduction surface. We assessed the temporal magnetic changes in the air, assuming the same remagnetising source within the volcano that was recently determined through ground surveys. We conclude that these expected temporal changes would reach a detection level in several years through a future survey in the air with the same autonomous vehicle.