Although negative interparental conflict predicts elevated externalizing problems for children, there are individual differences in this association. Theoretically, children’s abilities to coordinate physiological stress across response systems moderate the effects of interparental conflict on developmental outcomes. Past cross-sectional research has demonstrated that poor coordination of sympathetic (SNS) and parasympathetic (PNS) nervous systems puts children at a greater risk for externalizing behaviors in the context of interparental conflict. Our goal was to examine whether this same pattern is evident in adolescents and provide the first longitudinal test of this theoretical pathway. Participants were families with adolescents (10–17 years) from diverse ethnic and socioeconomic backgrounds. Parents reported conflict, were observed during a conflict discussion, and reported adolescent externalizing behaviors; parents again reported externalizing behaviors 1 year later. Adolescents experienced a stressor while skin conductance level (SCL; SNS) and respiratory sinus arrhythmia (RSA; PNS) were measured. Similar to past research with children, there were 3-way interactions between negative interparental conflict, SCL reactivity, and RSA reactivity in relation to adolescent externalizing behaviors, concurrently and prospectively. The overall pattern suggested that adolescents who displayed poorly coordinated responding displayed a positive association between interparental conflict and externalizing behaviors, whereas adolescents who showed well-coordinated responding displayed a nonsignificant or negative association. Coinhibition of the SNS and PNS may put adolescents particularly at risk for prospective externalizing behaviors. Autonomic nervous system coordination—particularly activation of the SNS and inhibition of the PNS during stress—may protect adolescents from experiencing adjustment problems in the context of interparental conflict.