Unlike many other water disinfection methods, hydroxyl radicals (HO•) produced by the Fenton reaction (Fe2+/H2O2) can inactivate pathogens regardless of taxonomic identity of genetic potential and do not generate halogenated disinfection by-products. Hydrogen peroxide (H2O2) required for the process is typically electrogenerated using various carbonaceous materials as cathodes. However, high costs and necessary modifications to the cathodes still present a challenge to large-scale implementation. In this work, we use granular activated carbon (GAC) as a cathode to generate H2O2 for water disinfection through the electro-Fenton process. GAC is a low-cost amorphous carbon with abundant oxygen- and carbon-containing groups that are favored for oxygen reduction into H2O2. Results indicate that H2O2 production at the GAC cathode is higher with more GAC, lower pH, and smaller reactor volume. Through the addition of iron ions, the electrogenerated H2O2 is transformed into HO• that efficiently inactivated model pathogen (Escherichia coli) under various water chemistry conditions. Chick–Watson modeling results further showed the strong lethality of produced HO• from the electro-Fenton process. This inactivation coupled with high H2O2 yield, excellent reusability, and relatively low cost of GAC proves that GAC is a promising cathodic material for large-scale water disinfection.