Interpersonal synchrony refers to alignment in time of interacting individuals. Recent neuroimaging findings indicate that the inferior frontal gyrus (IFG) — a core region of the observation-execution system — is not only activated during tasks that involve synchrony, but also coupled between interaction partners, suggesting a key role for the IFG in mediating interpersonal synchrony. In this study we investigated whether inter-brain synchrony (IBS) is modulated by inter-group relationships. We examined this question in the context of the Israeli-Palestinian conflict — one of the world’s most prolonged and intractable conflicts. Using functional Near Infra-Red Spectroscopy (fNIRS) hyperscanning, we measured IBS among ingroup vs. inter-group dyads (same-nationality dyads and Jewish-Palestinian dyads, respectively) while they performed a task entailing 2D movement synchrony. The results point to an increase in behavioral synchrony and greater enjoyment in the ingroup dyads, compared to the inter-group dyads. Critically, IBS in the left IFG significantly increased throughout task and it was higher among ingroup compared to inter-group dyads. Our findings highlight the effect of group membership on IBS plasticity.