This article deals with investigating the effect of cut-outs on the natural frequencies of magneto-electro-elastic (MEE) plates incorporating finite element methods based on higher order shear deformation theory (HSDT). In order to consider the influence of cut-out, the energy of the cut-out domain is sub-tracted from the total energy of the entire plate. The governing equations of motions are derived through incorporating Hamilton's principle and the solution is obtained using condensation technique. The proposed numerical formulation is verified with the results of previously published literature as well as the numerical software. In addition, this research focuses on evaluating the effect of geometrical skewness and boundary conditions on the frequency response. The influence of cut-outs on the degree of coupling between magnetic, electric and elasticfields is also investigated.