Josephson junctions with ferromagnetic barriers have been intensively investigated in recent years. Of particular interest has been the realization of so called π-junctions with a built-in phase difference, and induced triplet pairing. Such experiments have so far been limited to systems containing metallic ferromagnets. Although junctions incorporating a ferromagnetic insulator (I(F)) have been predicted to show a range of unique properties including π-shifts with intrinsically low dissipation and an unconventional temperature dependence of the critical current I(c), difficulties with the few known I(F) materials have prevented experimental tests. Here we report supercurrents through magnetic GdN barriers and show that the field and temperature dependence of I(c)is strongly modified by the I(F). In particular we show that the strong suppression of Cooper pair tunnelling by the spin filtering of the I(F) barrier can be modified by magnetic inhomogeneity in the barrier.