The electrical characteristics of Au/3C-SiC Schottky diodes were studied and related to crystal defects. A structural analysis performed by transmission electron microscopy (TEM), combined with a current mapping of the surface by conductive atomic force microscopy (C-AFM), indicated that stacking faults (SFs) are the conductive defects having the biggest influence on the electrical properties of the Schottky barrier on 3C-SiC. Further, C-AFM current mapping of the semiconductor surface also showed that an ultraviolet (UV) irradiation process enables the electrical passivation of the SFs, due to their preferential oxidation. From current-voltage (I-V) measurements in diodes of different area (different amount of defects) it was observed that, for the non-irradiated surface, no significant dependence of the Schottky barrier height (ΦB) on the contact area could be observed. On contrast, after the UV-irradiation, ΦB gradually increases with decreasing contact area, ultimately leading to a nearly ideal value of the barrier height for the smallest diodes. The results indicate that even after the passivation of SFs there are still some electrically active defects contributing to deleterious conduction, responsible for a worsening of the electrical properties of the diodes.