There are some archaeological sites with hard accessibility which remain unexplored and barely documented. The use of unmanned aerial systems (UAS) alleviates this challenge with aerial observations monitored with distant remote control. In addition to acquiring images in the visible wavelengths, other devices can be coupled on aerial platforms to inspect beyond the remaining structure of an archaeological site. For instance, thermography has proven to be of great help in the detection of buried remains due to observed temperature anomalies. This work explores the Castle of Puerta Arenas fortress to build the first aerial 3D reconstruction of this site by using RGB and thermographic images collected from a UAS. Orthomosaics have been applied to hypothesize about the original shape of the fortress, whereas 3D reconstructions have been rather applied to visualization and analysis. In this regard, the explored remains have been processed as dense point clouds in the visible and long-wave infrared spectrum, with the latter leading to the detection of hypothetical and still unknown towers. The detection of anomalies has been automatized by performing statistical analyses, globally and limited to smaller 3D voxel neighbourhoods. As a result, the studied remains have been documented and observed from an unexplored perspective, helping their conservation and dissemination, as well as suggesting future excavations.