Colorless polyimides (PIs) have been considered as potential substrates for flexible displays due to their excellent transparency, thermal stability, mechanical strength and flexibility. However, high water vapor transmission rate (WVTR) of PI films limits the lifetime of electronic devices using PI films as substrates. Two approaches were applied to reduce the WVTR of PI films. Graphene (RG), which is thermally reduced graphene oxide (GO), was blended with a nearly colorless PI solution synthesized from an alicyclic tetracarboxylic dianhydride and aromatic diamine in cosolvent to obtain PI/RG nanocomposites. Subsequently, a barrier thin film was deposited on those PI nanocomposites by radio frequency magnetron sputtering from a Si3N4 target. The deposited barrier layer was amorphous and its composition along the thickness was homogeneous based on the X-ray diffraction patterns and the depth profile by X-ray photoelectron spectroscopy. An optimum deposition thickness of the barrier layer is 30 nm to obtain a close-packed, smooth and continuous barrier film on PI. The presence of a 30 nm-thick barrier layer on PI/RG-0.1 nanocomposite film capably reduces the WVTR to 0.17 g/m2-day compared to 181 g/m2-day for pure PI and 13 g/m2-day for PI/RG-0.1. The surface of PI/RG is more hydrophobic and the capacity of moisture absorption by PI/RG is lower than PI/GO indicating the water resistance by RG is superior to that by GO. This flexible nanocomposite film remains high optical clarity and simultaneously shows excellent water barrier performance, enhanced dimensional stability and sufficient mechanical strength for advanced electronic applications.