Traditional paper and papermaking have struggled with a declining market during the last decades. However, the incorporation of nanotechnology in papermaking has brought possibilities to develop low-cost, biocompatible and flexible products with sophisticated functionalities. The functionality of nanopapers emerges from the intrinsic properties of the nanofibrous network, the additional loading of specific nanomaterials, or the additional deposition and patterning of thin films of nanomaterials on the paper surface. A successful development of functional nanopapers requires understanding in how the nanopaper matrix, nanomaterial fillers, coating pigments/inks, functional additives and manufacturing processes all interact to provide the intended functionality. This review addresses the emerging area of functional nanopapers. The review discusses flexible and multifunctional nanopapers, nanomaterials being used in nanopaper making, manufacturing techniques, and functional applications that provide new important possibilities to utilize papermaking technology. The interface where nanomaterials research meets traditional papermaking has important implications for food packaging, energy harvesting, and energy storage, flexible electronics, low-cost devices for medical diagnostics, and numerous other areas.