AbstractMetal‐free boron‐based catalysts such as boron oxide (B₂O₃) and boron nitride (h‐BN) are promising catalysts for methane oxidation to HCHO and CO. The B₂O₃ catalyst contains various probable boron sites (B¹ to B⁶), which may be responsible for methane oxidation. In this work, we utilized density functional theory to compare two relevant geometrically identical boron sites (B² and B⁴) for their reactivities. The two sites are explored in‐detail for the conversion of methane to formaldehyde (M2F), carbon monoxide and carbon dioxide. The B⁴ site activates the methane C−H bond easily as compared to the B² site. In M2F conversion, the rate‐determining step for the B² site is the co‐activation of dioxygen and methane, whereas over the B⁴ site, formaldehyde formation is the rate‐determining step. The computationally‐determined RDS for the B⁴ site coincides well with the reported experiments. It is further revealed that this site also prefers the formation of CO over CO₂, which is in‐line with the experiments in literature. It is also shown through orbital analysis that methanol formation does not occur during methane oxidation. We employed descriptors such as condensed Fukui functions and global electrophilicity index to chemically distinct these twin sites.