A novel method for the fabrication of silica/perfluoropolymer nanocomposites was investigated, whereby nano-sized silica particles without surface modification were dispersed uniformly through mechanical breakdown of loosely packed agglomerates of silica nanoparticles with low fracture strength in a polymer melt during direct melt-compounding. The method consists of two stages. The first stage involves preparation of the loose silica agglomerate, and the second stage involves melt-compounding of a completely hydrophobic perfluoropolymer, poly(tetrafluoroethyleneco-perfluoropropylvinylether), with the loose silica agglomerates prepared in the first stage. In the first stage, the packing structure and the fracture strength of the silica agglomerate were controlled by destabilizing an aqueous colloidal silica solution with a mean primary diameter of 190 nm via pH control and salt addition. In the next stage, the silica/perfluoropolymer nanocomposite was fabricated by breaking down the prepared loose silica agglomerates with low fracture strength by means of a shear force inside the polymer melt during melt-compounding.