The workpiece materials used in this study are CuNb nano-layered composites (NLC) which are produced in bulk form by accumulative roll bonding (ARB). CuNb NLC panels are of interest because of their increase in strength and radiation damage tolerance when compared to either of their bulk constituents. These increased properties stem from the bi-metal interface, and the nanometer length-scale of the layers. However to be commercially viable, methods to successfully join the ARB NLC which retain the layered structure panels are needed. Friction stir welding is investigated in this study as a possible joining method that can join the material while maintaining its layered structure and hence its properties. Mechanical properties of the weld were measured at a macro level using tensile testing, and at a local level via nano-indentation. The post weld layer structure was analyzed to provide insight into the flow paths. The grain orientation of the resulting weld nugget was also analyzed using electron backscatter diffraction and transmission Kikuchi diffraction. Results from this study show that the nano-layered structure can be maintained in the CuNb NLC by control of the friction stir welding parameters. The resulting microstructure is dependent on the strain experienced during the joining process. A variation in layer thickness reduction is correlated with increasing shear strain. Above a critical level of shear strain, the NLC microstructure was observed to fragment into equiaxed grains with a higher hardness than the NLC panels. Results from this study are also used to further the understanding of the material flow and hot working conditions experienced during the friction stir welding process.