This study was aimed at comprehensively investigating the utility of polymethyl methacrylate (PMMA) and CYTOP as encapsulation layers for flexible transparent electrodes composed of indium zinc tin oxide (IZTO). Optical modeling and experimental techniques were combined to assess the viability of PMMA and CYTOP as encapsulation materials. Optical modeling suggested that PMMA and CYTOP are well-suited for IZTO encapsulation. Subsequent experiment confirmed that the transmittance values of IZTO-films remained unaffected when encapsulated with PMMA and CYTOP. To examine the influence of encapsulation on mechanical resilience, all film, including untreated IZTO and IZTO treated with PMMA/CYTOP, were subjected to 20,000 bending cycles. The mechanical stability and optical properties of the IZTO film were considerably enhanced when encapsulated with these insulating materials. The improvement in transmittance was attributable to the lower refractive index of PMMA and CYTOP. Furthermore, scanning electron microscopy images demonstrated that the remarkable flexibility of PMMA and CYTOP effectively prevented the formation of cracks on the IZTO film, underscoring their pivotal role in enhancing the mechanical robustness of IZTO. In summary, this research highlights the potential of PMMA and CYTOP as efficient encapsulation materials for IZTO-based flexible transparent electrodes, offering dual benefits in terms of optical performance and mechanical durability.