In this study, amorphous manganese oxide (MnO2) nanostructured thin films were synthesized by a simple hydrothermal method. It is well known that the nanostructure plays a crucial role in energy storage applications. Herein, MnO2 nanostructures ranging from plates to flakes were synthesized without the use of any hard or soft templates. The 4+ oxidation state of Mn was confirmed by X-ray photoelectron spectroscopy. The MnO2 nanoflake structure has a specific surface area of 46 m2g−1, which provides it with an excellent rate capability and an exactly rectangular cyclic voltammogram (CV) curve. The MnO2 nanoflake electrode has a high specific capacitance of about 433 Fg−1, an energy density of 60 Whkg−1 at 0.5 mAcm−2, and an excellent cyclic stability of 95% over 1000 CV cycles in 1 M aq. Na2SO4. Kinetics analysis of the charge storage in the nanoflake MnO2 sample shows a 55.6% diffusion-controlled contribution and 44.4% capacitive-controlled contribution to the total current calculated at a scan rate of 100 mVs−1 from the CV curve.