A simple and effective method is given for the accurate extraction of the reflection coefficient in a discontinuity simulation of the rectangular waveguide by FDTD. It uses only the values of Ex-field on two adjacent cross sections of the waveguide under investigation. Neither a presolution of a related uniform waveguide nor the monomode transmission is needed, and a reflection coefficient is extracted from a single run of FDTD. The reference planes at which the voltage time records of the dominant mode are taken can be chosen very close to the discontinuity. This results in a substantial savings in CPU time and memory storage requirements.