By using the Wigner distribution function, the fractional Fourier transform (FRFT) of flat-topped multi-Gaussian (FTMG) beams is studied. Analytical expressions for the intensity distribution, beam width, far-field divergence angle,M2 factor and K parameter of FTMG beams are derived. The influence of fractional order on transformation properties of FTMG beams in the FRFT plane is illustrated with numerical examples.