A three dimensional elasticity analysis for the transverse free vibration characteristics of functionally graded magneto-electro-elastic plates based on the scaled boundary finite element method (SBFEM) incorporated with the precise integration algorithm (PIA) is presented. The material properties of magneto-electro-elastic plates are changing along the in-plane direction with arbitrary mathematical functions. In the proposed methodology, the strategies of only discretizing the in-plane surface and utilizing the two-dimensional spectral elements to construct diagonal coefficient matrices are adopted, which contributes to decreasing the calculation effort. The derivation process begins with the three dimensional governing equations of magneto-electro-elastic materials. Neither the plate mechanical kinematics nor invoking assumptions on the spatial distributions of electric and magnetic quantities are adopted. Built upon the introduced scaled boundary coordinates, the principle of virtual work and the technique of dual vectors, a first order ordinary differential SBFEM matrix equation for the in-plane functionally graded magneto-electro-elastic plates is obtained. Its general solution is analytically denoted as the matrix exponent. To improve the computation accuracy of the matrix exponent, the PIA is utilized to form the stiffness matrix. By virtue of the kinetic energy technique, it is convenient to construct the mass matrix of the in-plane functionally graded magneto-electro-elastic plates based on the SBFEM for the first time. Finally, comparisons of flexural frequency parameters with those from exact solutions and other numerical methods are provided. The accuracy, effectiveness, and versatility of the employed technique are validated. Moreover, additional numerical exercises are conducted to exhibit the influences of boundary conditions, material gradation functions, and aspect ratios on the free vibration behaviors of in-plane functionally graded magneto-electro-elastic rectangular, circular, and perforated plates.