GaN devices integrated with dissimilar substrates have transformed electronic and optoelectronic applications. However, an effective thermal resistance (TBReff) exists between the GaN layer and the dissimilar substrates typically, which can potentially cause a major heat transport bottleneck. A non-invasive method for monitoring the TBReff of bare wafers is a key enabler for process monitoring and for the reduction of TBReff through design optimization. The existing TBReff measurement techniques require metal deposition on the sample surface. Here, we demonstrate a generic non-invasive transient thermoreflectance technique which does not require modification of the GaN surface and can be applied to any GaN-based wafers, regardless of the substrate material. Above-bandgap pump and probe lasers are used to avoid any interference caused by sub-surface reflections, ensuring that this technique strictly follows the fundamental principle of thermoreflectance-based methods. Several GaN wafers on common substrates (SiC, Si, diamond, and sapphire) are measured to assess the validity of this technique.