Abstract: The measurement of the effective aperture of a waveguide antenna marked N5 is discussed in this paper. The principle and the method of measurement are presented. And the results of the effective aperture for the antenna with the corresponding frequencies are given. Compared to the results measured by Russian, the measured data is reliable. It facilitates the precisely measurement of the output power of the HPM source. The measurement method used in this paper can also be applied to measure the gain and the effective aperture of other antennas.