In this work, Gallium Nitride (GaN)-based p-i-n diodes were designed using a computer aided design (TCAD) simulator for realizing a betavoltaic (BV) cell with a high output power density (Pout). The short-circuit current density (JSC) and open-circuit voltage (VOC) of the 17 keV electron-beam (e-beam)-irradiated diode were evaluated with the variations of design parameters, such as the height and doping concentration of the intrinsic GaN region (Hi-GaN and Di-GaN), which influenced the depletion width in the i-GaN region. A high Hi-GaN and a low Di-GaN improved the Pout because of the enhancement of absorption and conversion efficiency. The device with the Hi-GaN of 700 nm and Di-GaN of 1 × 1016 cm−3 exhibited the highest Pout. In addition, the effects of native defects in the GaN material on the performances were investigated. While the reverse current characteristics were mainly unaffected by donor-like trap states like N vacancies, the Ga vacancies-induced acceptor-like traps significantly decreased the JSC and VOC due to an increase in recombination rate. As a result, the device with a high acceptor-like trap density dramatically degenerated the Pout. Therefore, growth of the high quality i-GaN with low acceptor-like traps is important for an enhanced Pout in BV cell.