The evolution equations of the gauge and Yukawa couplings are derived for the two-loop renormalisation group equations in a five-dimensional SM compactified on a $S^1/Z_2$ to yield standard four space-time dimensions. Different possibilities can be discussed, however, we shall consider the limiting case in which all matter fields are localised on the brane. We will compare our two-loop results to the results found at one-loop level, and investigate the evolution of $sin^2 theta_W$ in this scenario also.