Extant research on physiological dysregulation in children has focused on point-in-time measures and absolute mean levels of physiology. However, these methods do not capture dynamic fluctuations in physiology that characterize dysregulation. In the present work, we aimed to assess whether physiological dysregulation as captured by fluctuations rather than mean levels would differentiate between children with and without clinically elevated levels of externalizing behavior. As an exploratory approach, we examined fluctuations in children’s physiological responses (i.e., root mean square of successive differences [RMSSD] in beat-to-beat heart rate intervals) to social transgression scenarios across 15 short-term measurement occasions (5-second bins). Controlling for mean RMSSD, as well as emotional and cognitive correlates of externalizing behavior (i.e., sympathy and inhibitory control), children with externalizing difficulties exhibited greater within-person fluctuations in RMSSD (i.e., physiological dysregulation) compared to children without externalizing difficulties. The present findings provide preliminary support for using intensive longitudinal data comprised of short-term physiological measurements and point to the centrality of within-child physiological variability as a marker of dysregulation, particularly amongst children with externalizing disorders for whom self-regulation is a core challenge.