Validamycin A is an aminoglycoside fungicide produced by Streptomyces hygroscopicus that inhibits trehalase. The purpose of this study was to develop a method for detecting validamycin A in agricultural samples to establish MRL values for use in Korea. The validamycin A residues in samples were extracted using methanol/ water (50/50, v/v) and purified with a hydrophilic-lipophilic balance (HLB) cartridges. The analyte was quantified and confirmed by liquid chromatograph-tandem mass spectrometer (LC-MS/MS) in positive ion mode using multiple reaction monitoring (MRM). Matrix-matched calibration curves were linear over the calibration ranges (0.005~0.5 ng) into a blank extract with R2 > 0.99. The limits of detection and quantification were 0.005 and 0.01 mg/kg, respectively. For validation validamycin A, recovery studies were carried out three different concentration levels (LOQ, LOQ × 10, LOQ × 50, n = 5) with five replicates at each level. The average recovery range was from 72.5~118.3%, with relative standard deviation (RSD) less than 10.3%. All values were consistent with the criteria ranges requested in the Codex guidelines (CAC/GL 40-1993, 2003) and the NIFDS (National Institute of Food and Drug Safety) guideline (2016). Therefore, the proposed analytical method is accurate, effective and sensitive for validamycin A determination in agricultural commodities.