To develop an efficient and cost-effective cathodic electrocatalyst for microbial fuel cells (MFCs), carbon nanotubes (CNTs) coated with manganese dioxide using an in situ hydrothermal method (in situ MnO2/CNTs) have been investigated for electrochemical oxygen reduction reaction (ORR). Examination by transmission electron microscopy shows that MnO2 is sufficiently and uniformly dispersed over the surfaces of the CNTs. Using linear sweep voltammetry, we determine that the in situ MnO2/CNTs are a better catalyst for the ORR than CNTs that are simply mechanically mixed with MnO2 powder, suggesting that the surface coating of MnO2 onto CNTs enhances their catalytic activity. Additionally, a maximum power density of 210mWm−2 produced from the MFC with in situ MnO2/CNTs cathode is 2.3 times of that produced from the MFC using mechanically mixed MnO2/CNTs (93mWm−2), and comparable to that of the MFC with a conventional Pt/C cathode (229mWm−2). Electrochemical impedance spectroscopy analysis indicates that the uniform surface dispersion of MnO2 on the CNTs enhanced electron transfer of the ORR, resulting in higher MFC power output. The results of this study demonstrate that CNTs are an ideal catalyst support for MnO2 and that in situ MnO2/CNTs offer a good alternative to Pt/C for practical MFC applications.