The penetration of microwave power inside a human head model is improved by employing a dielectric loaded rectangular waveguide as the transmission source. A multi-layer reflection model is investigated to evaluate the combined material characteristics of different lossy human head tissues at 2.45 GHz. A waveguide loaded with a calculated permittivity of 3.62 is shown to maximise the microwave power penetration at the desired frequency. A Quartz (SiO2) loaded rectangular waveguide fed by a microstrip antenna is designed to validate the power penetration improvement inside an inhomogeneous human head phantom. A measured 1.33 dB power penetration increment is observed for the dielectric loaded waveguide over a standard rectangular waveguide at 50 mm inside the head, with an 81.9% reduction in the size of the transmission source.