The study presented in this article involves the estimation of the overall heat transfer coefficient of cooling system in RF capacitive hyperthermia treatment using inverse problem based on the conjugate gradient method to provide improved distribution of temperature. The temperature data computed numerically from the direct problem using the finite difference time domain method are used to simulate the temperature measurements. The effects of the errors and sensor positions upon the precision of the estimated results are also considered. The results show that a reasonable estimation of the unknown can be obtained. Finally, measurements in a tissue-equivalent phantom are employed to appraise the reliability of the presented method. The comparison of computed data with measurements shows a good agreement between numerical and experimental results.