This study investigated the role of autonomic nervous system (ANS) coordination in response to emotion in girls’ and boys’ development of relational (e.g., ignoring, excluding) and physical (e.g., hitting, kicking) aggression. Caregivers reported on children’s relational and physical aggression at ages 6, 7, 8, and 10 years (N = 232, 50.4% girls, 46.6% Latinx). Sympathetic nervous system (assessed via pre-ejection period) and parasympathetic nervous system (assessed via respiratory sinus arrhythmia) reactivity were measured in response to video clips depicting fear, happiness, and sadness at age 7. Growth curve models indicated that ANS reactivity to sadness, but not to fear or happiness, was related to trajectories of relational aggression. In contrast, ANS reactivity to all three emotions was associated with trajectories of physical aggression. Effects differed across genders, indicating that distinct patterns of ANS reactivity to emotion may be involved in girls’ and boys’ development of aggression. Overall, these findings contribute to a growing literature documenting the role of ANS reactivity to emotion in aggressive behavior. Moreover, this study considers ANS reactivity to specific emotions, as related to both relational and physical aggression, and as differentially expressed among girls versus boys.