In this study, for the use as a transparent electrode in flexible dye-sensitized solar cells (DSSCs), the indium zinc oxide (IZO) thin films on unheated poly(ethylene naphthalate) (PEN) substrate in pure argon ambient by radio frequency (RF) magnetron sputtering method have been prepared, and their characteristics with respect to RF power were investigated. It has been found that the IZO films on PEN show a dense amorphous structure and the surface microstructure of the films is hardly sensitive to the RF power. The electrical and optical properties of RF magnetron sputtered IZO thin films on PEN are strongly influenced by RF power. At a RF power of 60 W, it is obtained the IZO thin film with the sheet resistance of about 7.65 omega/sq. and optical transmittance of about 80% at 550 nm wavelength, resulting in the highest value for figure of merit. The flexible DSSC device embedded with the transparent IZO electrode deposited at 60 W shows the high power conversion efficiency, which is the value of 4.7% under simulated air mass 1.5 irradiation.