Humans show a rare tendency to punish norm-violators who have not harmed them directly—a behavior known as third-party punishment. Research has found that third-party punishment is subject to intergroup bias, whereby people punish members of the out-group more severely than the in-group. Alhough the prevalence of this behavior is well-documented, the psychological processes underlying it remain largely unexplored. Some work suggests that it stems from people’s inherent predisposition to form alliances with in-group members and aggress against out-group members. This implies that people will show reflexive intergroup bias in third-party punishment, favoring in-group over out-group members especially when their capacity for deliberation is impaired. Here we test this hypothesis directly, examining whether intergroup bias in third-party punishment emerges from reflexive, as opposed to deliberative, components of moral cognition. In 3 experiments, utilizing a simulated economic game, we varied participants’ group relationship to a transgressor, measured or manipulated the extent to which they relied on reflexive or deliberative judgment, and observed people’s punishment decisions. Across group-membership manipulations (American football teams, nationalities, and baseball teams) and 2 assessments of reflexive judgment (response time and cognitive load), reflexive judgment heightened intergroup bias, suggesting that such bias in punishment is inherent to human moral cognition. We discuss the implications of these studies for theories of punishment, cooperation, social behavior, and legal practice.