Atomic layer deposited AlGaN with different AlN and GaN pulse ratios (2:1, 1:1, and 1:2) was used to prepare AlGaN/GaN Schottky diodes, and their current transport mechanisms were investigated using current–voltage (I–V) and capacitance–voltage (C–V) measurements. Under low reverse bias condition, the sample with the pulse ratio of 2:1 was explained by Poole–Frenkel emission and the negative temperature dependence for the sample with the pulse ratio of 1:2 was associated with the acceptor levels in the AlGaN layer. Fast interface traps at 0.24–0.29 eV were observed for the samples with the pulse ratios of 1:1 and 1:2, whereas bulk traps at ~0.34 eV were observed for the sample with the pulse ratio of 2:1. Higher trap densities were obtained from the C–V hysteresis measurements when the pulse ratios were 1:1 and 1:2, indicating the presence of a charge trapping interfacial layer. According to the X-ray photoelectron spectroscopy spectra, the pulse ratio of 2:1 was found to have less oxygen-related defects in the AlGaN layer.