Coaxial‐microstrip transition sections are extensively used in radio frequency (RF) circuits, providing electrical interconnection and signal transmission. However, an antipad used for impedance compensation in the coaxial‐microstrip transition section leads to signal return path discontinuity and radiation emission. Accordingly, in this current work, the impact of impedance compensation structure on the near‐field radiation in the coaxial‐microstrip transition section was investigated by theoretical analysis and experimental testing. A 3D electromagnetic field model of a circuit board with an anti‐pad was developed to calculate the S‐parameters and radiation electric field. Based on the characteristics of the electric near‐field probe, a transfer function model was also developed to convert the radiation electric field obtained by the electromagnetic field model into the output voltage for better comparison with the test results. In addition, the effect of the rise time of the input signal on near‐electric field radiation was also studied in this work. The experimental results are in good agreement with the simulation results obtained from the transfer function model. The results of this study provide a better understanding of the electromagnetic radiation characteristics caused by the impedance compensation structure and theoretical support for compensation optimization strategy in engineering.