The nitrogen‐polar GaN material system is a promising candidate for high‐frequency applications, such as those in the millimeter‐wave range. Schottky barrier height is one of fundamental parameters necessary for device applications of N‐polar GaN. Herein, vertical Schottky diodes for both N‐polar and Ga‐polar GaN are prepared, and it is found through experiments that the barrier height of N‐polar GaN is smaller than that of Ga‐polar GaN by 0.21 V. This difference in the barrier height stems from the polarization‐induced surface charge layer of a few angstroms thickness under the surface. Numerical calculation of band profiles suggests that a significant band bending caused by the large amount of polarization charges pushes the conduction band energy downward (upward) in the N‐polar (Ga‐polar) surface depending on the sign of the polarization charges, which results in two different effective Schottky barrier heights. This difference is explained by assuming the polarization‐charge layer thickness of about 5 Å. A simple analytical model to estimate the difference in barrier heights between the two polarities is also proposed.