Molecular dynamics simulations are used to study the diffusion of polymer-grafted nanoparticles (PGNPs) in polymer. The diffusivity of PGNPs in the homopolymer matrix is investigated as a function of graft length and grafting density, and it is compared to that of bare nanoparticles with comparable effective size. Our results indicate that, in addition to the increase in the effective size of PGNPs due to grafting, the interpenetration of matrix polymers into the grafted layer also plays an important role in the mobility of PGNPs. In systems consisting of both PGNPs and bare particles, the spatial arrangement of the bare particles was found to be having a significant influence on the mobility of PGNPs. At low graft length and high grafting density, the matrix chains dewets the grafted layer, due to autophobic dewetting, creating a sharper interface between the matrix and the grafted layer. The bare particles then migrate to the interface creating a barrier around the PGNPs that hinders the matrix-graft interpenetration and results in the higher mobility of PGNPs. Our results emphasize the importance of polymer-particle interface on the dynamic properties of polymer nanocomposites.