In this work, a novel microfluidic-based method using a miniaturized chemical analysis system was developed for the determination of synthetic antioxidants in edible oils. Having capitalized on the end-channel amperometric detection using a SU8/glass microchip electrophoresis, three interesting phenolic antioxidants in olive and sunflower oils were studied, including tert-butyl hydroquinone (TBHQ), butylated hydroxyanisole (BHA), and propyl gallate (PG). The length of the separation channel was 40 mm, depth and width of the channel were 20 and 50 μm, respectively. Three miniaturized Au electrodes were used as the electrochemical detection system having 50, 250 and 250 μm width for working, counter and pseudo-reference electrodes, respectively. First, the electrochemical behavior of antioxidants was studied on the carbon screen-printed electrode. Second, the parameters that affect the separation were investigated. Finally, at the optimum separation conditions, the analytes were separated. The injection was carried out using +850 V for 8 s and the separation and detection voltages were set at +1000 V and +1 V, respectively. The quality of the method was evaluated through its analytical figures of merit and by the comparison of the proposed method by HPLC-DAD. The linear range for the detection of analytes was 10–100 μM for TBHQ, BHA and 20–200 μM for PG without any pretreatment of analytes. The correlation coefficients for all the analytes were in good range and the obtained results were in good agreement to those obtained by the HPLC method.