In the pursuit of high capacity anode materials transition metal oxides have paid great deal of attention. However poor electronic conductivity, high discharge potential and volume change during electrochemical cycling hinders their practical applications. In this report, we synthesize the well-ordered mesoporous β-MnO2 phases (pyrolusite structure) using SBA-15 and MCM-48 templates. The product derived from SBA-15, designated as SBA-MnO2 has interconnected nanorod like morphology, whereas the product derived from MCM-48, designated as MCM-MnO2 exhibits open cage/bowl like morphology. The products are characterized by XRD, FTIR, FESEM, TEM, XPS, BET surface area measurements. Further, electrochemical studies are carried out to investigate their application as anode material for Li-ion batteries. Galvanostatic cycling shows initial discharge capacity of ∼1500 mAhg−1 and 1750 mAhg−1 respectively for SBA-MnO2 and MCM-MnO2. After 100 charge-discharge cycles, MCM-MnO2 electrode exhibits capacity ∼ 345 mAhg−1 and SBA-MnO2 shows a capacity of ∼ 245 mAhg−1. Though both the materials show capacity fading upon long cycling, their performance is better compared to other MnO2 nanostructures reported in the literature. They also exhibit good rate capability indicating that mesoporous MnO2 materials reported here can be potential candidate for Li-ion storage.