We study the deviation of yukawa coupling in the gauge-Higgs unification scenario from the Standard Model one. Taking into account the brane mass terms necessary for generating the flavor mixing and removing the exotic massless fermions, we derive an analytic formula determining the KK mass spectrum and yukawa coupling. Applying the obtained results to the tau and bottom yukawa couplings, we numerically calculate the ratio of the yukawa couplings in the gauge-Higgs unification and in the Standard Model.