The electrochemical production of H2O2via the two-electron oxygen reduction reaction (2e− ORR) has recently attracted attention as a promising alternative to the current anthraquinone process. Identification of active sites in O-doped carbon materials, which exhibit high activities and selectivities for the 2e− ORR, is important for understanding the selective electrocatalytic process and achieving the rational design of active electrocatalysts. However, this is impeded by the heterogeneous distribution of various active sites on these catalysts. In this study, we exploited the molecular functionalisation approach to implant anthraquinone, benzoic acid, and phenol groups on carbon nanotubes and systematically compared the electrocatalytic activities and selectivities of these functional groups. Among these oxygen functional groups, the anthraquinone group showed the highest surface-area-normalised and active-site-normalised activities.