Human peer relations provide tangible benefits, including food and protection, as well as emotional benefits. While social exclusion poses a threat to all of these benefits, the psychological threat is particularly susceptible to modulation by the relation of the excluders to the excluded person. The current study used functional magnetic resonance imaging to explore the effects of manipulating the gender relation of participants to their excluders during an interactive ball-toss game. Ventral anterior cingulate cortex activation was higher during exclusion by same-gender peers, while right ventrolateral prefrontal cortex activation negatively correlated with self-reported distress in other-gender exclusion. Results imply that exclusion by one's own gender is fundamentally different from exclusion by the opposite gender, and suggest a regulatory role for ventrolateral prefrontal cortex in response to out-group exclusion. Individual differences in implicit gender attitudes modulated neural responses to exclusion. The importance of these findings to investigations of social cognition is discussed.