The fractional Fourier transform (FRFT) of the flat-topped multi-Gaussian beam (FMGB) is investigated based on the three kinds of FRFT optical systems: Lohmann I, Lohmann II, and quadratic graded-index systems. The analytical expressions for the FRFT of the FMGB are derived based on the propagation of the FMGB through the three systems. By introducing a hard-edge aperture function, the analytical expressions for the FRFT of the FMGB carried out by the apertured FRFT optical systems are presented. The FRFT characteristics of the FMGB for the three kinds of FRFT optical systems with and without apertures are discussed in detail. Results show that the three types of FRFT optical systems have the same function when the apertures are ignored but that significantly different characteristics are exhibited when the apertures appear.