Gauge-Higgs unification is the fascinating scenario solving the hierarchy problem without supersymmetry. In this scenario, the Standard Model (SM) Higgs doublet is identified with extra component of the gauge field in higher dimensions and its mass becomes finite and stable under quantum corrections due to the higher dimensional gauge symmetry. On the other hand, Yukawa coupling is provided by the gauge coupling, which seems to mean that the flavor mixing and CP violation do not arise at it stands. In this talk, we discuss that the flavor mixing is originated from simultaneously non-diagonalizable bulk and brane mass matrices. Then, this mechanism is applied to various flavor changing neutral current (FCNC) processes via Kaluza-Klein (KK) gauge boson exchange at tree level and constraints for compactification scale are obtained.