We have developed a technique for the site-selective electroless deposition of Cu on poly(ethylene terephthalate) (PET) substrate modified with an organic self-assembled monolayer (SAM). The PET substrate was first modified with a silica-like layer by being dip-coated in an acetone solution of 3-aminopropyltrimethoxysilane and treated with UV light. The PET substrate was further modified with thiol groups using a 3-mercaptopropyltrimethoxysilane-SAM and then irradiated by UV light through a photomask to prepare thiol-group regions and OH-group regions. Cu was then deposited on only the thiol-group regions of the substrate by electroless deposition in a neutral solution with no catalysts by using dimethylamineborane as a reducing reagent. This site-selective deposition process can control the deposition conditions by an organic thin film fabricated on a surface-modified PET substrate, and thus can be applied to other low heat-resistant substrates.