By using the method of generalized Huygens-Fresnel diffraction integral, the analytical expression for the cross-spectral density of partially coherent flat-topped beams propagating in the gradient-index media has been derived. Consequently, the propagation properties of partially coherent flat-topped beams propagating in the gradient-index media have been studied. Moreover, the influence of the gradient-index parameter of media, the beam order and the beam coherence on the propagation properties has been discussed. The results show that the on-axis intensity distribution of partially coherent flat-topped beams propagating in the gradient-index media varies periodically. The period depends on the gradient-index parameter, but has no relation with the beam coherence. The on-axis peak intensity in media increases with the beam order, the beam coherence parameter, and the gradient-index parameter of media. Furthermore, the intensity distribution near the plane of peak intensity varies rapidly with the propagation distance.