In this article, we introduce a method for fabricating highly conductive transparent poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) thin nano-structured film by treating the pristine PEDOT:PSS film with concentrated (55%) hydroiodic acid (HI). HI treatment on the pristine PEDOT:PSS film could significantly reduce the film sheet resistance without sacrificing its transparency and other electronic properties, which are highly desirable for transparent conductors. A thin layer of HI treated PEDOT:PSS film (74 nm) has very high transmittance of 90% and a low sheet resistance of 95 ohm sq(-1). The sheet resistance of the film can be reduced to 37 ohm sq(-1) by increasing the film thickness but at the expense of its transparency. The low sheet resistance of the film can be attributed to the increase of polarons density, conformational changes and formation of clusters due to removal of some PSS from PEDOT:PSS particles. The results were confirmed by the UV/VIS/near-IR absorption spectroscopy, atomic force microscopy, X-ray photoelectron spectroscopy and energy-dispersive X-ray spectroscopy. Given the high electrical conductivity of the HI treated PEDOT:PSS film, it was then tested as a transparent organic cathode in a polymer solar cell. This ITO-free solar cell showed superior current generation and charge collection with an efficiency of 5.83%, which is 18 times higher than the cell that used untreated PEDOT:PSS film. We, therefore, envisage this potential fabrication method, which uses HI acid, to be applied on other conjugated polymers to enhance their conducting properties for practical applications.