In civil engineering, usually the methods used to estimate the thickness of thin pavements consider flat interfaces for simplification. In this paper, the roughness of the surfaces is taken into account. First, the amplitudes of the first two echoes from the rough thin pavement are calculated from a rigorous electromagnetic method, the PILE method. A comparison is then made with the flat interface case, and their differences in the electromagnetic backscattering are highlighted. Eventually, the influence of the pavement roughness on the pavement thickness estimation is investigated by using the Maximum Likelihood Method.