A disposable cover for electromagnetic treatment applicators prevents undesired exposure to potentially harmful radiation. The cover is a pouch-like structure having a back surface (which faces opposite, or away from, the treatment area) constructed from shielding material, such as metallized polyethylene. At least a portion of the cover which faces the treatment area is constructed solely from non-shielding material. Adhesive strips, ZIP-LOCK®, or other interlocking edges, secure the applicator inside the cover and close off any leaks. The electromagnetic properties of the cover are integrated into the circuitry for the treatment applicator, such that the applicator is not functional in the absence of the cover. In use, an electromagnetic treatment applicator is inserted into the cover and positioned over the area to be treated, with the non-shielding, or “window”, portion of the cover overlying the treatment area. Once assembled, the applicator/cover combination forms a closely matched and tuned network for effecting a highly efficient RF output. When activated, the generated electromagnetic energy only exits the cover through the opening or “window”, thereby preventing exposure of the patient or caregiver to potentially harmful radiation.