A breast cancer hyperthermia system has been developed for the targeted of increasing hyperthermia therapy efficiency after lumpectomy surgery with the assistance of fat grafting technique. Enhancing the efficiency of hyperthermia treatment will decrease the required radiation doses after surgery. A fat grafting technique is applied around the tumor region that is located into glandular tissue for the purpose of enhancing wave penetration through glandular tissue. The proposed hyperthermia system employs a single horn antenna operating at 2.45 GHz. Here, a modified hyperthermia system was tested on a hemisphere phantom of two different densities with various tumor sizes at depth 2.8 cm from skin layer. Transmission and reflection coefficients of applied electromagnetic waves at the air‐phantom interface were calculated analytically.