Recently, Fermi-LAT detected GeV emission during the X-ray flaring activity in GRB 100728A. We study various scenarios for its origin. The hard spectrum of the GeV emission favors the external inverse-Compton origin in which X-ray flare photons are up-scattered by relativistic electrons in the external forward shock. This external IC scenario, with anisotropic scattering effect taken into account, can reproduce the temporal and spectral properties of the GeV emission in GRB 100728A.