In this paper, we first review the most common measurement methods, previously used, for assessing the complex permittivity of human skin, namely, open-ended coaxial and waveguide probe reflectometry methods. We then outline and emphasize their useful features and shortcomings that can adversely affect the measurements. Then, an approach utilizing an open-ended waveguide probe with an engineered ground plane and a thin dielectric layer in front of the aperture to prevent skin protrusion is proposed. This approach utilizes a full-wave electromagnetic model that accurately describes the interaction of a layered skin with this probe. Furthermore, comprehensive analyses were performed to investigate the important sources of modeling and measurement errors and their influences on the calculated skin complex permittivity. The results of these analyses have shown that the proposed method can achieve ~85% and ~95% calculation accuracy for skin relative (to free space) dielectric constant and relative dielectric loss factor, respectively. Finally, a series of in vivo measurement was performed in the Ka-band (26.5–40 GHz) on several different locations of three human subjects using this proposed method. In addition, it is demonstrated that the homogeneous skin model cannot be used for areas of the body where the stratum corneum (SC) layer is relatively thick (e.g., palm). Finally, the effect of a thick SC layer on the relative complex permittivity calculation was discussed, and a modified method to determine the relative complex permittivity of the layered skin was proposed and verified by simulations.