Unmanned aerial systems (UASs) have been already proven to be useful in fields and disciplines such as agriculture, forestry, or environmental mapping, and they have also found application during natural and nuclear disasters. In many cases, the environment is inaccessible or dangerous for a human being, meaning that the widely used technique of aerial imagery georeferencing via ground control points cannot be employed. The present article introduces a custom-built multi-sensor system for direct georeferencing, a concept that enables georeferencing to be performed without an access to the mapping area and ensures centimetre-level object accuracy. The proposed system comprises leading navigation system technologies in the weight category of micro and light UASs. A highly accurate Global Navigation Satellite System receiver integrating the real-time kinematic technology supports an inertial navigation system, where data from various sensors are fused. Special attention is paid to the time synchronization of all sensors, and a method for the field calibration of the system is designed. The multi-sensor system is completely independent of the used UASs. The authors also discuss the verification of the proposed system’s performance on a real mission. To make the results credible, a high number of test points are used, with both direct and indirect georeferencing techniques subjected to comparison, together with different calibration methods. The achieved spatial object accuracy (about 4 cm root mean square error (RMSE)) is sufficient for most applications.