In this study, the charge transport mechanism of Pd/Si-based FS-GaN Schottky diodes was investigated. A temperature-dependent current−voltage analysis revealed that the I-V characteristics of the diodes show a good rectifying behavior with a large ratio of 103−105 at the forward to reverse current at ±1 V. The interface states and non-interacting point defect complex between the Pd metal and FS-GaN crystals induced the inhomogeneity of the barrier height and large ideality factors. Furthermore, we revealed that the electronic conduction of the devices prefers the thermionic field emission (TFE) transport, not the thermionic emission (TE) model, over the entire measurement conditions. The investigation on deep level transient spectroscopy (DLTS) suggests that non-interacting point-defect-driven tunneling influences the charge transport. This investigation about charge transport paves the way to achieving next-generation optoelectronic applications using Si-based FS-GaN Schottky diodes.