RNA is one of suitable biomaterials for the fabrication in nanoscale, because of its ability to self-assemble. Naturally occurring RNA often interacts with proteins, facilitating and regulating the formation of functional molecular complexes in cells. We focused on RNA-protein complex (RNP) to design and construct synthetic nanostructures, because RNP nanostructures have a potential to form complicated structures with sophisticated functions. Here we review our designed RNP nanostructures and possible biological applications. Functional molecules can be introduced into the RNP nanostructures and applied to control functions of mammalian cells. These RNP nanostructures can expand the field of nanotechnology, biomedicine and synthetic biology.