Electrical characterizations of AlGaN/GaN heterojunctions isolated by N implantation at elevated temperatures were investigated. Three-terminal measurements were carried out to characterize leakage paths, and crystal lattice damage due to implantation was monitored by high-resolution x-ray diffraction. Compared with room temperature implantation, the current leakage was reduced by ∼103 times by the implantation at 300 °C. The low leakage was attributed to low acceptor-like energy levels due to low crystal lattice damage by the “dynamic annealing” effect at high-temperature implantation. The post-annealing process increased the current leakage by two orders of magnitude. This indicates that the implantation isolation process should be conducted after higher temperature processes (>450 °C) in the fabrication of GaN devices. These results can provide valuable information for the fabrication, reliability, and mass production of various GaN-based photonics and electronics.