We analyze the electroweak phase transition at finite temperature in a model of gauge-Higgs unification where the fermion mass hierarchy including top quark mass, a viable electroweak symmetry breaking and an observed Higgs mass are successfully reproduced. To study the phase transition, we derive the general formula of the 1-loop effective potential at finite temperature by using the $zeta$ function regularization method. It is remarkable that the functions determining the Kaluza-Klein mass spectrum have only to be necessary in calculations. This potential can be applicable to any higher dimensional theory in flat space where one extra spatial dimension is compactified. Applying to our model of gauge-Higgs unification, the strong first phase transition compatible with 125 GeV Higgs mass is found to happen.