This study investigates leakage mechanisms in vertical GaN-on-GaN Schottky barrier diodes (SBDs) and demonstrates effective mitigation strategies. The fabricated devices exhibit low reverse leakage current (1 × 10−5 A/cm2 at −200 V) and a high Ion/Ioff ratio (∼1010), surpassing the performance of GaN SBDs on foreign substrates. We elucidate dominant leakage mechanisms—thermionic emission, Poole–Frenkel emission, and variable-range hopping—and their evolution with temperature and bias. Optimized fabrication processes, including defect etching and a novel dual-layer passivation technique, achieve over a 1000-fold reduction in leakage current.