Photovoltaic cells can convert incoming sunlight within their responsive wavelength range into electricity. Unfortunately, the majority of the incident radiation is reflected, absorbed directly as heat, or indirectly converted to heat due to internal losses (i.e., ≥ 52.9%, even world-record efficiency cells). In concentrated photovoltaic systems, this added heat can further degrade the electrical conversion efficiency of the cells if it is not removed, resulting from an elevated operating temperature. Spectral splitters and absorptive filters can remove the unused portion of the solar spectrum before it is converted to heat in the photovoltaic cells and harvest this energy for active use in thermal applications. In this paper, an innovative concentrated photovoltaic/thermal system that utilizes a layered design containing an optical fluid and a phase change material was investigated as a new alternative absorptive filter. Five possible configurations of this filter were compared from energy, exergy, and energy storage perspectives. These layers consist of a phase change material (dotriacontane, a paraffin) layer and fluid channel layers (a glycerol fluid) with suspended Ag and/or Au nanoparticles. The optical properties of the nanofluid and the nano-enhanced phase change material (NEPCM) were modeled using Mie and Rayleigh scattering theories. The comparison showed that the configuration containing the nanofluid channel at the top of the nano-enhanced phase change material performs well in all aspects of energy, exergy, and energy storage. A parametric study was conducted to determine the effects of nanoparticles volume fraction, concentration ratio, mass flow rate, nanofluid thickness and phase change material thickness on PV/T system performance with this filter configuration. It was found that volume fractions lower than 0.3 × 10−5 and 0.2 × 10−5 for Ag and Au, respectively, provided the best system performance for the assumed geometric and operational conditions. At an optimal mass flow of 0.005 kg s−1 for the nanofluid, this design achieved a maximum exergetic efficiency of 24% for a concentration ratio of 30. The results also revealed that the nanofluid-NEPCM filter is not suitable for concentration ratios of less than 10. Overall, this study finds that nanofluid-NEPCM-based spectral splitter, in addition to successfully filtering radiation, can store energy efficiently.