Tame and aggressive rat lines were created during the long-term selection of Norway rats for elimination and enhancement of aggressiveness toward humans, respectively. Our previous experiments have demonstrated that selection for the elimination of defensive aggression toward humans is associated with attenuated intraspecific intermale aggression. However, the neuronal mechanisms underlying low and high intermale aggression in the tame and aggressive rats remain unclear. Here, we used c-Fos immunoreactivity to evaluate neuronal activation patterns in the main aggression-related areas in selected lines under basal conditions and after the resident–intruder (R–I) test. Although agonistic behavior of the tame and the aggressive rats differed significantly, social encounter caused similar brain activation patterns in both groups; we observed increased neuronal activation in the bed nucleus of stria terminalis, the hypothalamic attack area, and the medial amygdala 1h after the R–I test. However, neuronal activation in the hypothalamic attack area was significantly higher in the aggressive males compared to their tame counterparts. We propose that lower activation of the hypothalamic area is associated with the attenuation of intraspecific intermale aggression during selection for the elimination of aggressiveness toward humans.