Mesoporous silica SBA-15 supported iron and cobalt catalysts (Fe–Co/SBA-15) were prepared and used in the electrochemical (EC) enhanced heterogeneous activation of peroxydisulfate (PDS, S2O82−) process for the removal of Orange II. The effects of some important reaction parameters such as initial pH, current density, PDS concentration and dosage of Fe–Co/SBA-15 catalysts were investigated. The results showed that the decolorization efficiency was not significantly affected by the initial pH value, and it did increase with the higher PDS concentration, current density and Fe–Co/SBA-15 dosage. Both the sulfate radical (SO4·−) and the hydroxyl radical (OH) are considered as the primary reactive oxidants for the Orange II decolorization. The Fe–Co/SBA-15 catalyst maintained its high activity during repeated batch experiments. The intermediate products were identified by GC–MS analysis and a plausible degradation pathway is proposed accordingly. The removal efficiencies of chemical oxygen demand (COD) and total organic carbon (TOC) were 52.1% and 31.9%, respectively after 60 min of reaction time but reached 82.9% and 51.5%, respectively when the reaction time was extended to 24 h. Toxicity tests with activated sludge indicated that the toxicity of the solution increased during the first 30 min and then decreased as the oxidation proceeded. Display omitted •Fe–Co/SBA-15 was fabricated and utilized in EC enhanced heterogeneous activation of PDS.•The effect of reaction parameters for the decolorization of Orange II was evaluated.•Possible reaction mechanism and the stability of Fe–Co/SBA-15 were investigated.•Main intermediates were determined and a plausible degradation pathway was proposed.•The toxicity of Orange II was eliminated after 24 h treatment.