The internal standard method using ion chromatography combined with tandem mass spectrometry (IC-MS/MS) for quantifying perchlorate in different types of food was established. Because the presence of ions and other biomolecules in matrices usually interrupts accurate determination of perchlorate, it is necessary to develop efficient, reproducible method to determine perchlorate concentrations in food. In this study, the internal standard method was compared with the external standard method to determine perchlorate concentrations in standard samples. The obtained method detection limit (MDL) for perchlorate was 0.005 µg/L for bottled water, 0.12 µg/L for milk, 0.27 µg/kg for rice, 0.16 µg/kg for vegetables, and 0.07 µg/kg for seaweed, respectively. The limit of quantitation (LOQ) was calculated by multiplying the MDL by 7. The recoveries of perchlorate from food samples spiked with perchlorate ranged from 98 to 105% and their percent relative standard deviation (%RSD) levels were <20%. This method was successfully applied for the quantitative determination of perchlorate in various kinds of food.