We report first-principles simulation of polarization mechanisms in hydroxyapatite to explain the underlying mechanism behind the reported ion conductivities and polarization under electrical poling at elevated temperatures. It is found that ion conduction occurs mainly in the column of OH⁻ ions along the c-axis through a combination of the flipping of OH⁻ ions, exchange of proton vacancies between OH⁻ ions, and the hopping of the OH⁻ vacancy. The calculated activation energies are consistent with those found in conductivity measurements and thermally stimulated depolarization current measurements.