Upconversion nanoparticles (UCNPs) have attracted great interest due to their unique properties such as anti-Stokes shift, high biocompatibility, and photostability compared with other fluorophores. Single UCNP-based studies are important for highly sensitive biosensing and bioimaging. To enhance the photoluminescence (PL) intensity of UCNPs, various plasmonic nanostructures have been investigated in addition to engineering the elements and structures of UCNPs themselves. However, it is crucial but challenging to precisely control the position of a single UCNP relative to plasmonic nanostructures. Herein, gold nanorod dimers (GNRDs) are used to enhance the PL intensity of single UCNPs selectively captured in the gaps of GNRDs. The dimensions of GNRDs are designed with the assistance of COMSOL Multiphysics simulation to have a plasmonic resonance peak around the excitation wavelength for the UCNPs. After lithography-based fabrication of GNRDs and surface passivation, electron-beam induced deposition is used to selectively create carbon nanodomains (CNDs) in the gaps of GNRDs. The CNDs capture UCNPs by benefiting from the strong affinity between streptavidin and biotin. About 12% of the CNDs capture single UCNPs. Photoluminescence imaging shows an overall intensity enhancement by threefold for single UCNPs by GNRDs of 100 nm gap at 4 × 10 6 W / cm 2 power density. This study shows a promising route for single UCNP-based studies, especially when it is needed to control the position of single UCNPs.