We show that a flavour symmetry a la Froggatt-Nielsen can be naturally incorporated in models with gauge-Higgs unification, by exploiting the heavy fermions that are anyhow needed to realize realistic Yukawa couplings. The case of the minimal five-dimensional model, in which the SU(2)(L) x U(1)(Y) electroweak group is enlarged to an SU(3)(W) group, and then broken to U(1) em by the combination of an orbifold projection and a Scherk-Schwarz twist, is studied in detail. We show that the minimal way of incorporating a U(1)(F) flavour symmetry is to enlarge it to an SU(2)(F) group, which is then completely broken by the same orbifold projection and Scherk-Schwarz twist. The general features of this construction, where ordinary fermions live on the branes defined by the orbifold fixed- points and messenger fermions live in the bulk, are compared to those of ordinary four-dimensional flavour models, and some explicit examples are constructed.