Riboflavin (vitamin B2) immobilized multiwalled carbon nanotubes modified electrode (GCE/MWCNT@RB) has been prepared and demonstrated as a selective and sensitive electrocatalytic flow injection analysis electrochemical sensor for iodate detection. The GCE/MWCNT@RB modified electrode showed a highly stable and well defined surface confined redox peak at an E_1/2 = 155 ± 20 mV vs. Ag/AgCl with a surface excess value of 4.72 nmol cm⁻². Physicochemical and electrochemical characterizations reveal the presence of surface confined riboflavin sites on GCE/MWCNT system. At an applied potential = −0.1 V vs Ag/AgCl, hydrodynamic flow rate = 800 μL min⁻¹ and phosphate buffer (pH 2) as a carrier solution condition, the analytical characteristics such as stability, repeatability, linear range and detection limit were described. The relative standard deviation of successive 29 injections of 25 μM of iodate was 3.61%. Iodate calibration plot was linear in a range of 25–750 μM with regression coefficient, sensitivity and limit of detection (S/N = 3) of 0.9998, 0.77 μA mM⁻¹ and 2.7 μmol L⁻¹ (9.4 ng/20 μL) respectively. The new system showed absence of interference with iodide, chloride, nitrate, bromate and perchlorate. Quantitative detection of iodate in iodized table salts was further demonstrated.