Poorly crystalline porous δ-MnO2 is synthesized by hydrothermal route from a neutral aqueous solution of KMnO4 at 180°C and the reaction time of 24h. The as-synthesized sample and also the sample heated at 300°C have nanopetals morphology with large surface area. On heating at temperatures ⩾400°C, there is a decrease in BET surface area and also a change in morphology from nanopetals to clusters of nanorods. Furthermore, the poorly crystalline δ-MnO2 converts into well crystalline α-MnO2 phase. The electrochemical lithium intercalation and de-intercalation studies in a non-aqueous electrolyte provide a high discharge specific capacity (275mAhg−1) at a specific current of 40mAg−1 for the poorly crystalline δ-MnO2 samples. The rate capability is also high. There is a decrease in capacity on repeated charge–discharge cycling. The specific capacity values of the crystalline α-MnO2 samples are considerably less than the values of poorly crystalline δ-MnO2 samples. Thus, the hydrothermal route facilitates preparation of poorly crystalline electrochemically active porous MnO2.