We study proton decay in a supersymmetric SO(10) gauge theory in six dimensions compactified on an orbifold. The dimension-5 proton decay operators are forbidden by R-symmetry, whereas the dimension-6 operators are enhanced due to the presence of KK towers. Three sequential quark-lepton families are localised at the three orbifold fixed points, where SO(10) is broken to its three GUT subgroups. The physical quarks and leptons are mixtures of these brane states and additional bulk zero modes. This leads to a characteristic pattern of branching ratios in proton decay, in particular the suppression of the p → µ + K 0 mode.