Material thermal conductivity is a key factor in various applications, from thermal management to energy harvesting. With microstructure engineering being a widely used method for customizing material properties, including thermal properties, understanding and controlling the role of extended phonon-scattering defects, like grain boundaries, is crucial for efficient material design. However, systematic studies are still lacking primarily due to limited tools. In this study, we demonstrate an approach for measuring grain boundary thermal resistance by probing the propagation of thermal waves across grain boundaries with a temperature-sensitive scanning probe. The method, implemented with a spatial resolution of about 100 nm on finely grained Nb-substituted SrTiO3 ceramics, achieves a detectability of about 2 × 10-8 K m2 W-1, suitable for chalcogenide-based thermoelectrics. The measurements indicated that the thermal resistance of the majority of grain boundaries in the STiO3 ceramics is below this value. While there are challenges in improving sensitivity, considering spatial resolution and the amount of material involved in the detection, the sensitivity of the scanning probe method is comparable to that of optical thermoreflectance techniques, and the method opens up an avenue to characterize thermal resistance at the level of single grain boundaries and domain walls in a spectrum of microstructured materials.