A nitrogen-polarity (N-polarity) GaN-based high electron mobility transistor (HEMT) shows great potential for high-frequency solid-state power amplifier applications because its two-dimensional electron gas (2DEG) density and mobility are minimally affected by device scaling. However, the Schottky barrier height (SBH) of N-polarity GaN is low. This leads to a large gate leakage in N-polarity GaN-based HEMTs. In this work, we investigate the effect of annealing on the electrical characteristics of N-polarity GaN-based Schottky barrier diodes (SBDs) with Ni/Au electrodes. Our results show that the annealing time and temperature have a large influence on the electrical properties of N-polarity GaN SBDs. Compared to the N-polarity SBD without annealing, the SBH and rectification ratio at ±5 V of the SBD are increased from 0.51 eV and 30 to 0.77 eV and 7700, respectively, and the ideal factor of the SBD is decreased from 1.66 to 1.54 after an optimized annealing process. Our analysis results suggest that the improvement of the electrical properties of SBDs after annealing is mainly due to the reduction of the interface state density between Schottky contact metals and N-polarity GaN and the increase of barrier height for the electron emission from the trap state at low reverse bias.