We have developed a compact desktop-sized nanopatterning system driven by the Roll-to-Roll (R2R) nanoimprinting (NIL) principle. The system realizes the continuous and high-speed stamping of various nanoscale patterns on a large-area flexible substrate without resorting to ponderous and complicated instruments. We first lay out the process principle based on continuous NIL on a UV-curable resin layer using a flexible nanopatterned mold. We then create conceptual and specific designs for the system by focusing on two key processes, imprinting and UV curing, which are performed in a continuous R2R fashion. We build a system with essential components and optimized modules for imprinting, UV curing, and R2R conveying to enable simple but effective nanopatterning within the desktop volume. Finally, we demonstrate several nanopatterning results such as nanolines and nanodots, which are obtained by operating the built desktop R2R NIL system on transparent and flexible substrates. Our system may be further utilized in the scalable fabrication of diverse flexible nanopatterns for many functional applications in optics, photonics, sensors, and energy harvesters.