Nitrogen-doped graphitic carbon has been intensively studied for potential use as an electrocatalyst in fuel cells for the oxygen reduction reaction (ORR). However, the lack of a mechanistic understanding on the carbon catalysis has severely hindered the progress of the catalyst development. Herein we use a well-defined graphene nanostructure as a model system and, for the first time, reveal an oxygen activation mechanism that involves carbanion intermediates in these materials. Our work shows that the overpotential of the electrocatalytic ORR is determined by the generation of the carbanion intermediates, and the current by the rate the intermediates activate oxygen.