We show a perturbation theory of the Josephson transport through ferromagnetic insulators (FIs). Recently we have found that the appearance of the atomic scale 0–π transition in such junctions based on numerical calculations. In order to explore the mechanism of this anomalous transition, we have analytically calculated the Josephson current using the tunneling Hamiltonian theory and found that the spin dependent π-phase shift in the FI barrier gives the atomic scale 0–π transition.