The present work is to investigate the variations in antioxidant activity of Cordyceps militaris grown using the submerged cultivation. The activities of intracellular antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT), and the antioxidant abilities of water and ethanol extracts of cultured C. militaris were tested. The intracellular oxidative stress in C. militaris was significantly increased after 3 days’ cultivation. However, for most of the enzymes and extracts, the antioxidant activity time profiles did not follow the trend of oxidative stress. There were great variations in the antioxidant activities, possibly due to the different requirements of the cells during cultivation. The results also suggest that C. militaris resisted the damage from superoxide anion mainly with SOD, and resisted the damage from hydrogen peroxide with both CAT and antioxidant compounds.