Broccoli, one of Brassica vegetables, has been known to possess various health beneficial activities including anti-inflammation, anti-oxidation and anti-cancer etc. Various metabolites were indicated as active compounds in broccoli. Glucosinolates such as glucoraphanin, glucobrassicin, glucoerucin and isothiocyanates, i.e. sulforaphane, which is produced through the enzymatic action of myrosinase are getting focus as their bioactivities. In this study, we treated broccoli with pulsed electric field (PEF) processing and the metabolite profiles were investigated based on the metabolomics analysis. PEF process was applied to stem and floret of broccolis with three different levels; 500, 1000, 1500 pulses with 2 kV/cm, then metabolites were extracted with 70% methanol. Metabolomic analysis was carried out with mass spectrometry through multivariate statistical analysis based on the OPLS-DA model. Significant changes of metabolite profiles were observed by PEF treatment and specific metabolites were affected as dose dependent manner. Content of major glucosinolates compounds such as glucoerucin, glucoiberin, glucoraphanin, glucobrassicin, 4-hydroxy glucobrassicin, and 4-methoxy glucobrassicin were significantly reduced, while sulforaphane was distinctively increased in PEF treated broccolis. The results implied that myrosinase released from vacuole by PEF processing transformed glucosinolate into isothiocyanate, which would be useful findings for enhancing bioactivity of broccoli by simple PEF treatment.