The patterning of gold nanoparticles (GNPs) on the surface of a fluoropolymer substrate by using patterned surface grafting and layer-by-layer deposition techniques is described. The surface of a poly(tetrafluoroethylene-co-perfluorovinyl ether) (PFA) substrate was selectively implanted with 150 keV proton ions. Peroxide groups were successfully formed on the implanted PFA surface, and their concentration depended on the fluence. Acrylic acid was graft polymerized onto the implanted regions of the PFA substrate, resulting in well-defined patterns of poly(acrylic acid) (PAA) on the PFA substrate. The surface properties of the PAA-patterned PFA surface, such as chemical compositions, wettability, and morphology, were investigated. The surface analysis results revealed that PAA was definitely present on the implanted regions of the PFA surface, and the degree of grafting was dependent on three factors: fluence, grafting time, and monomer concentration. Furthermore, GNP patterns were generated on the prepared PAA-patterned PFA surface by layer-by-layer deposition of GNPs and poly(diallyldimethyl ammonium chloride). The multilayers of GNPs were deposited only onto the PAA-grafted regions separated by bare PFA regions, and the resulting GNP patterns exhibited good electrical conductivity.