In this research, we present a novel design for a large scale spectral splitting concentrator photovoltaic system based on double flat waveguides. The sunlight concentrator consists of a Fresnel lens array and double waveguides. Sunlight is firstly concentrated by Fresnel lenses then reaches an upper flat waveguide (UFW). The dichroic mirror-coated prisms are positioned at each focused area to divide the sunlight spectrum into two bands. The mid-energy (mid E) band is reflected at the prism surface and coupled to the UFW. The GaInP/GaAs dual-junction solar cell is attached at the exit port of the UFW to maximize the electrical conversion efficiency of the mid E band. The low-energy (low E) band is transmitted and reaches a bottom flat waveguide (BFW). The mirror coated prisms are utilized to redirect the mid E band sunlight for coupling with the BFW. The GaInAsP/GaInAs dual-junction solar cell is applied to convert the low E band to electricity. The system was modeled using the commercial optic simulation software LightTools™. The results show that the proposed system can achieve optical efficiencies of 84.02% and 80.01% for the mid E band and low E band, respectively, and a 46.1% electrical conversion efficiency for the total system. The simulation of the system performance and comparison with other PV systems prove that our proposed design is a new approach for a highly efficient photovoltaic system.