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The electrochemical degradation of ibuprofen (IBP) by electro-Fenton process has been studied in a flow-through system by evaluating the performance of two different iron sources, sacrificial cast iron anode and FeSO4 salt. The effect of operating conditions, including initial IBP concentration, cast iron anode location, initial FeSO4 concentration, applied current, the split current on the iron anode, solution pH, and flow rate on the efficacy of the process was evaluated. The sequence of the electrodes significantly influences ibuprofen removal. When using cast iron anode as iron source, placing the iron anode upstream achieved the best IBP removal rate. Split current of 3 mA applied on the iron anode out of 120 mA total current is the optimum current for remove 1 mg/L of IBP under a flow rate of 3 mL/min. There is a linear correlation between the applied current and the Fe2+ concentration in the FeSO4-system. The initial IBP concentration does not influence the rate of Fenton reaction. Flow rate influences the degradation efficiency as high flow rate dilutes the concentration of OH radicals in the electrolyte. FeSO4-system was less affected by the flow rate compared to the iron anode-system as the concentration of the Fe2+ was steady and not diluted by the flow rate. Both systems prefer acidic operation conditions than neutral and alkaline conditions. Iron-anode can be used as an external Fe2+ supply for the treatment for iron-free. These findings contribute in several ways to our understanding of the electro-Fenton process under flow conditions and provide a basis for how to design the reactor for the water treatment.