Summary: A method for estimating complex permittivity of a material using a rectangular waveguide with a flange is presented by the finite difference time domain (FDTD) method. An advantage of the present method is that it is not necessary to vary the material structure in order to insert it into the waveguide. Therefore estimation errors related to the dimensions of the material are almost negligible. In this case, fluoridated rubber is chosen as the low-loss material. The comparison of the complex permittivity of the material determined by the present method with FDTD and the conventional waveguide method at 10 GHz is performed. It was confirmed that the present method is effective for estimating the complex permittivity under the condition that the length of the flange is about 50 mm (1.7λ) square.