Hypothyroidism is an autoimmune disease associated with underactive thyroid gland. In this study, a dual effect polymeric system was designed to release Cepharanthine (CEP) to block T cell activation and Selenium (Se) to decrease the anti-thyroid peroxidase (TPOAb) concentration in order to treat hypothyroidism. For this purpose, poly(ethylene-vinyl acetate) (PEVA) and polyethylene glycol (PEG) nanoparticles (NPs) including CEP were synthesized by emulsion solvent evaporation method and they were loaded to polyurethane (PU)/PEG-PUSe-PEG block copolymer blends which were fabricated by particulate leaching technique as porous sponges. Fourier-Transform Infrared (FTIR), Raman, and Nuclear Magnetic Resonance (NMR) analysis showed successful synthesis of PEG-PUSe-PEG block copolymer. A long-term zero-order release profile was obtained for CEP. Se release rate from matrices showed an oxidative stress-mediated release which can be used to adjust Se amount. According to MTS results conducted by NIH 3T3 fibroblasts, both NPs and matrices have no adverse effect on cell viability. Fluorescence microscopy and SEM images confirm the MTS results. The dual release system has potential to be effectively used in long-term treatment of hypothyroidism by addressing both auto-immune response and hormone regulation.