6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC) is a bioactive ingredient present in wasabi, a popular pungent spice in Japan. Previous studies have revealed the cytoprotective and cancer chemopreventive effects of 6-MSITC. This study aims to clarify the molecular mechanisms by investigating the action of 6-MSITC on the Nrf2/Keap1 system. 6-MSITC up-regulated the expression of NAD(P)H:quinone oxidoreductase 1 (NQO1) by increasing the Nrf2 level. Treatment with 6-MSITC extended the half-life (t1/2) of Nrf2 protein from 11.5 to 35.2 min, approximately three times longer. Moreover, 6-MSITC suppressed the ubiquitination of Nrf2 but not Keap1. Alternatively, a modified Keap1 was observed in 6-MSITC-treated cells accompanying reduction of normal Keap1 protein. The results from cellular fractionation and immunocytochemistry assay revealed that Nrf2 was primarily accumulated in nucleus. EMSA and the reporter gene assay further demonstrated that 6-MSITC augmented Nrf2-ARE binding and transcription activity. Silencing Nrf2 using Nrf2 siRNA markedly reduced the Nrf2 level and ARE-driven activity under both baseline and 6-MSITC-induced conditions. Our data revealed that 6-MSITC enhanced Nrf2/ARE-driven NQO1 expression by stabilizing Nrf2 that was accomplished by modifying Keap1 with consequent inhibition of the ubiquitination and proteasomal turnover of Nrf2. The findings provide an insight into the mechanisms underlying 6-MSITC in cytoprotection and cancer chemoprevention.