The dispersion stability of silica aggregates in the rubber matrix is one of the concerns for silica-filled compounds. Silica aggregates tend to flocculate due to their poor compatibility with the rubbers and consequent strong tendency for self-association. The flocculation process can occur during compound storage as well as at the onset of vulcanization. This present work studies the kinetics of the flocculation process in silica-reinforced natural rubber (NR) compounds by following the changes of the storage modulus during thermal annealing under conditions applied for vulcanization. The results demonstrate that silica flocculation can be effectively suppressed by increasing compound dump temperature and amount of silane, as these result in a better degree of dispersion, higher degrees of hydrophobation, and filler–rubber interaction. The compounds containing highly dispersible silicas exhibit greater filler–rubber interaction, but their flocculation processes develop faster when compared to the compounds filled with conventional silicas. Epoxidation of NR clearly influences the filler–rubber interaction but shows no clear evidence of a change of flocculation rate.