Transcranial Doppler ultrasound (TCD) is a method that uses a hand held low frequency (2-2.5 MHz), pulsed Doppler phased array probe to measure blood velocity within the arteries located inside the brain. The problem with TCD lies in the low ultrasonic energy penetrating inside the brain through the skull which leads to low signal to noise ratio. This is due to several effects including phase aberration, variations in the speed of sound in the skull, scattering, the acoustic impedance mismatch and absorption of the three layer medium constituted by soft tissues, the skull and the brain. The goal of this paper is to study the effect of transmission losses due to the acoustic impedance mismatch on the transmitted energies as a function of frequency. To do so, wave propagation was modelled from the ultrasonic transducer into the brain. This model calculates transmission coefficients inside the brain, leading to a frequency-dependent transmission coefficient for a given skin and bone thickness. This approach was validated experimentally by comparing the analytical results with measurements obtained from a bone phantom plate mimicking the skull. The average position error of the occurrence of the maximum amplitude between the experiment and analytical result was equivalent to a 0.06 mm error on the skin thickness given a fixed bone thickness. Similarity between the experimental and analytical result was also demonstrated by calculating correlation coefficients. The average correlation between the experimental and analytical result came out to be 0.50 for a high frequency probe and 0.78 for a lower frequency probe. Further analysis of the simulation showed that an optimized excitation frequency can be chosen based on skin and bone thicknesses, thereby offering an opportunity to improve the image quality of TCD.