Aeromagnetic with Unmanned Aerial Vehicle (UAV) has a variety of advantages compared to the traditional method, i.e. using airplanes or helicopters. With the advancement of UAVs technology, magnetic sensors have also been developed for installation on UAVs. However, these sensors are heavy, expensive, and have high power consumption. These drawbacks magnify while using aeromagnetic gradiometry which needs measurements with two sensors simultaneously. We propose to apply a cost-effective, light, low power consumption MEMS sensor with a reasonable resolution on a UAV. For validation, we compare the result with a terrestrial survey with a proton magnetometer. This comparison shows the great capability of MEMS sensors for metallic ore resources prospecting.