Different B-doped rGO catalysts were prepared and their 2e- oxygen reduction reaction (ORR) performance was investigated. It was found that the 2e- ORR selectivity of B-doped rGO was related to the B content and oxygen mass transfer conditions. The synthesized catalyst exhibited high 2e- ORR selectivity of 95–98.6%, and the H2O2 yield reached up to 95.63 mg cm−2 h−1 at a current density of 200 mA cm−2. Moreover, increasing the oxygen concentration in the gas supplied to the B-doped rGO modified gas diffusion electrode (GDE) only to 30–40% resulted in almost the same H2O2 yield as using pure oxygen. Experimental analysis and theoretical calculations indicated that the isolated B dopant acts as active site for the 2e- ORR. Furthermore, B-doped rGO modified GDE was applied to the electro-Fenton system to continuously degrade organic pollutants. This work will be beneficial for the study and application of carbon-based ORR catalysts.