The effective diffusion coefficient of radon is a very important factor in estimating the rate of radon exhalation from the ground surface. In this study, we developed an experimental system that overcomes technical problems in previous studies to accurately evaluate the effective diffusion coefficient. The radon source used for this system was the National Institute of Radiological Sciences radon chamber. This chamber is a calibrated international standard facility that can produce stable radon concentrations for long periods of time. Our tests showed that leakage of radon from the system was negligible. After the leakage test, we evaluated the effective diffusion coefficient in free-space and in dry porous materials at porosities of 35% and 45%. To ensure that the porous material in the column was as homogeneous as possible, we filled the column with an artificial soil with controlled grain size and grain composition. The measured values and theoretical calculations agreed well, which indicate that the proposed system can be used to accurately and quickly evaluate the effective diffusion coefficient.