BaZrO3 exhibits excellent proton conductivity and good high‐temperature stability. It is therefore a promising electrolyte material for solid oxide fuel cells. The stability of BaZrO3 at high temperatures is generally explained by the low diffusivity of O vacancy. Present first principle density functional theory calculations show that the slow migration of the doubly charged O vacancy at high temperature cannot be solely caused by the ground‐state migration energy but by the contribution of phonon excitations to the free migration energy. With increasing temperature, the effective barrier for oxygen vacancy migration increases. At about 1000 K, which is the operating temperature of fuel cells, the calculated O vacancy diffusivity is more than one order of magnitude lower than that determined using ground‐state migration barrier. The calculated diffusivity data agree well with experimental results from literature. The present work reveals that the high‐temperature stability of BaZrO3 is mainly due to the phonon contribution to the free migration energy of the O vacancy.