A coupled system of the photo-Fenton advanced oxidation technique and an aerobic sequential batch reactor (SBR) was used to treat wastewater from biodiesel production using either palm or castor oil. The photo-Fenton reaction and biological process were evaluated individually and were effective at treating the wastewater; nevertheless, each process required longer degradation times for the wastewater pollutants compared with the coupled system. The proposed coupled photo-Fenton/aerobic SBR system obtained a 90% reduction of the chemical oxygen demand (COD) in half of the time required for the biological system individually.