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In this study, the electrochemical degradation process of 5-fluorouracil (5-FU) in aqueous media was performed using a continuous flow reactor in an undivided cell (system I), and in a divided cell with a cationic membrane (Nafion ® 424) (system II). In system I , 75% of 5-FU degradation was achieved (50 mg L −1 ) with a applied current density j app  = 150 A m −2 , volumetric flow rate qv  = 13 L h −1 , after 6 h of electrolysis (k app  = 0.004 min −1 ). The removal efficiency of 5-FU was higher (95%) when the concentration was 5 mg L −1 under the same conditions. Nitrates (22% of initial amount of N), fluorides (27%) and ammonium (10%) were quantified after 6 h of electrolysis. System II , 77% of 5-FU degradation was achieved (50 mg L −1 ) after 6 h of electrolysis (k app  = 0.004 min −1 ). The degradation rate of 5-FU was complete when the concentration was 5 mg L −1 under the same conditions. Nitrates (29% of initial amount of N), fluorides (25%) and ammonium (5%) were quantified after 6 h of electrolysis. In addition, the main organic byproducts identified by mass spectroscopy were aliphatic compound with carbonyl and carboxyl functionalities. Due to, the mineralization of 5-FU with acceptable efficiency of 88% found in system II ( j app of 200 A m −2 ), this system seems to be more promising in the cytostatic drug removal. Moreover the efficiency of 5-FU removal in diluted solutions is better in system II than in system I. [ABSTRACT FROM AUTHOR]