A generalized Langevin equation with fluctuating diffusivity (GLEFD) is proposed, and it is shown that the GLEFD satisfies a generalized fluctuation-dissipation relation. If the memory kernel is a power law, the GLEFD exhibits anomalous subdiffusion, non-Gaussianity, and stretched-exponential relaxation. The case in which the memory kernel is given by a single exponential function is also investigated as an analytically tractable example. In particular, the mean-square displacement and the self-intermediate-scattering function of this system show plateau structures. A numerical scheme to integrate the GLEFD is also presented.