Metal oxide based transition metals and its alloys are among one of the most prospective non- platinum grade candidates that can be possibly used as electrocatalysts in low temperature (LT) operating fuel cell devices. They possess favorable structural hierarchy with eminently conducting porous networks and large surface area for catalytic activity. Manganese dioxide (MnO₂) have been investigated for a variety of application in environment and energy, however very little study has been done on MnO₂ nanorods as an electrode catalyst for fuel cell. Herein MnO₂ nanorods have been synthesized by hydrothermal method and thermal treated with various temperatures (300,400 and 500 ⁰C), oxygen vacancies were thermally induced during heat treatment. The MnO2 nanorods were investigated for oxygen vacancies under high angular dark field (HAADF). It is vivid from X-ray photoelectron spectroscopy (XPS) analysis that the oxygen vacancies on the MnO2 nanorods were increased and hardened with the rise in temperature. The MnO2 nanorods (treated at 400 ⁰C) showed the best performance toward oxygen reduction reaction (ORR), excellent stability and highest methanol tolerance as compared to commercial Pt/C in acidic media. These characteristics were imparted to the MnO2 nanorods due to the preferential growth on (211) index and optimized oxygen vacancies impregnation. It was also shown that MnO₂ nanorods stretched to become thinner and longer with the increasing effect of temperature. These investigations suggest that MnO₂ nanorods are thermal sensitive materials and their performance for ORR can be increased under optimized temperature.