Josephson junctions with ferromagnetic barriers have been intensively investigated in recent years(1). Of particular interest has been the realization of so called pi-junctions with a built-in phase difference(2), and induced triplet pairing(3,4). 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 pi-shifts with intrinsically low dissipation(5,6) and an unconventional temperature dependence(7) 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.