Methyl tert-butyl ether (MTBE) is always the most likely found compound at the front of a gasoline plume due to its chemical characteristics. In this study, an iridium dioxide (IrO2) coated electrode was utilized to perform electrochemical removal of MTBE in a lab-scale bath electrolyzer. Depending on the constant-potential controls, electrochemical removal of MTBE can be conducted either through direct oxidation, water electrolysis competition, or indirect oxidation. Direct oxidation mechanism performed MTBE removal up to 39% as electrolyzing below 1.2 V, and the occurrence of water electrolysis competition dropped MTBE removal as increasing the operative potential up to 2.0 V. The continual increase of operative potential above 2.0V brought about indirect oxidation of MTBE through the chain reactions of the redox mediator S2O8 2−/SO4 2−. The matrix effect of iron enhances electrochemical oxidation of MTBE to provide about 2 times improvement on MTBE removal. The products of MTBE degradation were identified as tert-butyl alcohol (TBA), acetone, and CO2 by GC/MS, and the distributions of carbon atoms in TBA, acetone, CO2, and MTBE were found 18, 12, 62, and 8% through the optimum control of electrochemical oxidation.