Nakajimana (Brassica rapa L. cv. nakajimana), of the family Brassicaceae, is a traditional vegetable in Japan. Three isothiocyanates and five cyanides in the leaves of nakajimana were identified by gas chromatography (GC) and GC-mass spectrometry (GC-MS), and their kinetic changes using heat-treatment (temperature and time) were investigated. In addition, myrosinase activity of extracts prepared from fresh nakajimana leaf was determined. In crushed heat-treated leaves of nakajimana (70 °C for 30 s), formation of isothiocyanates and myrosinase activity increased, whereas formation of 1-cyano-3,4-epithiobutane and 1-cyano-4,5-epithiopentane decreased. Heat-treatment can significantly alter the content of potentially beneficial compounds in nakajimana, and ingestion of suitable isothiocyanates for human health may be better facilitated by mild boiling.