Wurtzite BAlN alloy with large bandgap is an emerging material system for UV optoelectronic and power devices. In this study, the BAlN/GaN heterojunction with a sharp interface and uniform distribution of the elements was formed by careful control of epitaxial conditions to avoid GaN desorption and parasitic reactions whose band alignment was then measured for the first time. The valence band offset (VBO) was found to be nearly-zero, i.e. −0.2 ± 0.2 eV, in the B0.14Al0.86N/GaN heterojunction by X-ray photoelectron spectroscopy. Additionally, the conduction band offset (CBO) is estimated at 2.1 ± 0.2 eV, which is the largest reported CBO among epitaxial GaN-based heterojunctions. In comparison to the type-I Al0.75Ga0.25N/GaN heterojunction (both Al0.75Ga0.25N and B0.14Al0.86N alloy have the same bandgap of 5.7 eV), the CBO and VBO of the B0.14Al0.86N/GaN heterostructure are significantly larger and smaller, respectively. The nearly-zero VBO and the very large CBO of the B0.14Al0.86N/GaN heterojunction could potentially lead to considerable performance enhancement for GaN optoelectronics and power electronics devices.