Brain mechanisms for the refractory period that characteristically follows ejaculation in animals and human are poorly understood. The possibility of active inhibition of brain areas being responsible for the post-ejaculatory inhibitory state has not been ruled out. Using Blood Oxygen Level Dependent (BOLD) functional magnetic resonance imaging (fMRI) we have mapped brain areas in healthy young volunteers immediately after ejaculation. Functional imaging of the brain for 30 minutes beginning after three minutes of ejaculation induced by masturbation showed spatio-temporal activation in amygdala, temporal lobes and septal areas. The septal areas were observed to be active for a shorter duration than the amygdala and the temporal lobe. Thus the temporal sequence of involvement of the above neural structures may contribute to temporary inhibition of sexual arousal/penile erection during the post-ejaculatory refractory period in humans.