GaN substrates are promising candidates for GaN high electron mobility transistors (HEMTs) due to their epitaxial layer growth with a low defect density. In this study, technology computer-aided design simulations were executed to design the GaN HEMTs on semi-insulating GaN substrates with thin channel layers. Traps in the GaN substrates played a role in suppressing drain-leakage currents, although degrading transient responses changed the bias from off to on-state for the 0.02-μm thin channel layer. A trade-off relationship between the drain-leakage current and transient response is occurred by changing the trap concentration in the GaN substrates. The AlGaN back-barrier structure has been found to be highly effective in suppressing the drain-leakage current in low-trap-concentration GaN substrates. The trade-off relationship improved by adopting the back-barrier layers, and the maximum drain current decreased. The drain-current reduction compensated by increasing the Al content in the barriers without degrading the trade-off relationship. Therefore, for GaN HEMTs that have low-trap-concentration GaN substrates combined with the back-barrier layer, a high-Al-content barrier have characteristics that are favorable for the trade-off relationship in the case of thin channel layers. Moreover, the traps in GaN substrates were found to affect low-frequency S21, which is important for linearity of the power amplifier, as critically as the transient responses.