Changes occur in brain functions before, during and after physical exercise as well as during orthostasis in males and females. The study aimed at understanding the effect of gender on post-exercise orthostasis induced changes in EEG amplitudes. 30 apparently healthy individuals consisting of 15 males (18.5 years) and 15 females (18.5years) were recruited for the study. They were divided into baseline, exercise and post-exercise orthostasis groups. Subjects were exercised on a treadmill for 10 minutes at 8km/hr. After which they were asked to stand for 10 minutes on both legs. EEG recording was carried out using PowerLab 26T using frontal and occipital electrodes as indicated in the operational manual. When compared with baseline, post-exercise orthostasis caused reduction in theta waves amplitude in males and females respectively and a decrease in alpha waves amplitude in males only. Post-exercise orthostasis lowered theta waves amplitude in males when compared with females while other EEG waves were not affected. There was a positive correlation was observed between shock index and alpha wave amplitude (r= 0.437, P<0.05) in males during post-exercise orthostasis but none in female. The findings of the study indicated that orthostasis after exercise relatively reduced theta waves in males compared to females.