A novel stopped flow injection—amperometric (sFI-Amp) procedure for determination of chlorate has been developed. The reaction of chlorate with excess potassium iodide and hydrochloric acid, forming iodine/triiodide that is further electrochemically reduced at a glassy carbon electrode at +200 mV versus Ag/AgCl electrode is employed. In order to increase sensitivity without using of too high acid concentration, promoting of the reaction by increasing reaction time and temperature can be carried out. This can be done without increase of dispersion of the product zone by stopping the flow while the injected zone is being in a mixing coil which is immersed in a water bath of 55 ± 0.5 °C. In a closed system of FIA, a side reaction of oxygen with iodide is also minimized. Under a set of conditions, linear calibration graphs were in the ranges of 1.2 × 10⁻⁶–6.0 × 10⁻⁵ mol l⁻¹and 6.0 × 10⁻⁵–6.0 × 10⁻⁴ mol l⁻¹. A sample throughput of 25 h⁻¹ was accomplished. Relative standard deviation was 2% (n = 21, 1.2 × 10⁻⁴ mol l⁻¹ chlorate). The proposed sFI-Amp procedure was successfully applied to the determination of chlorate in soil samples from longan plantation area.