Both cortical and parasympathetic systems are believed to regulate emotional arousal in the service of healthy development. Systemic coordination, or coupling, between putative regulatory functions begins in early childhood. Yet the degree of coupling between cortical and parasympathetic systems in young children remains unclear, particularly in relation to the development of typical or atypical emotion function. We tested whether cortical (ERN) and parasympathetic (respiratory sinus arrhythmia [RSA]) markers of regulation were coupled during cognitive challenge in preschoolers ( = 121). We found no main effect of RSA predicting ERN. We then tested children's typical and atypical emotion behavior (context-appropriate/context-inappropriate fear, anxiety symptoms, neuroendocrine reactivity) as moderators of early coupling in an effort to link patterns of coupling to adaptive emotional development. Negative coupling (i.e., smaller ERN, more RSA suppression larger ERN, less RSA suppression) at age 3 was associated with greater atypical and less typical emotion behaviors, indicative of greater risk. Negative age 3 coupling was also visible for children who had greater Generalized Anxiety Disorder symptoms and blunted cortisol reactivity at age 5. Results suggest that negative coupling may reflect a maladaptive pattern across regulatory systems that is identifiable during the preschool years.