Exogenous methyl jasmonate (MeJA) treatment was known to increase the levels of neoglucobrassicin and their bioactive hydrolysis products in broccoli ( Brassica oleracea var. italica ), but the fate of MeJA-induced glucosinolates (GSLs) after various cooking methods was unknown. This study measured the changes in GSLs and their hydrolysis compounds in broccoli treated with MeJA and the interaction between MeJA and cooking treatments. All cooked MeJA-treated broccoli contained significantly more GSLs than untreated broccoli ( p < 0.05). After 5 min of cooking (boil, steam, microwave), MeJA-treated broccoli still contained 1.6- to 2.3-fold higher GSL content than untreated broccoli. Neoglucobrassicin hydrolysis products were also significantly greater in steamed and microwaved MeJA-treated broccoli. The results show that exogenous MeJA treatment increases neoglucobrassicin and its hydrolysis compounds in broccoli even after cooking. Once the positive and negative effects of these compounds are better understood, the results of this experiment can be a valuable tool to help food scientists, nutrition scientists, and dieticians determine how to incorporate raw or cooked broccoli and Brassica vegetables in the diet.