A new method to simultaneously analyze various glucosinolates (GSLs) and isothiocyanates (ITCs) by reversed-phase ultra-high-performance liquid chromatography-electron spray ionization-tandem mass spectrometry has been developed and validated for 14 GSLs and 15 ITCs. It involved derivatization of ITCs with N-acetyl-l-cysteine (NAC). The limits of detection were 0.4-1.6 μM for GSLs and 0.9-2.6 μM for NAC-ITCs. The analysis of Sinapis alba, Brassica napus, and Brassica juncea extracts spiked with 14 GSLs and 15 ITCs indicated that the method generally had good intraday (≤10% RSD) and interday precisions (≤16% RSD). Recovery of the method was unaffected by the extracts and within 71-110% for GSLs and 66-122% for NAC-ITCs. The method was able to monitor the enzymatic hydrolysis of standard GSLs to ITCs in mixtures. Furthermore, GSLs and ITCs were simultaneously determined in Brassicaceae plant extracts before and after myrosinase treatment. This method can be applied to further investigate the enzymatic conversion of GSLs to ITCs in complex mixtures.