There is growing interest among educational researchers in using heart rate variability (HRV) as an index of children's capacity to regulate their physiological arousal. Links between HRV and young children's self-regulation have, however, been inconsistent, and there is limited research on children's HRV in learning-related contexts. HRV was collected from 86 children aged 3.41 to 5.83 years before, during, and after they engaged in a learning interaction with an examiner. Higher HRV during a pre-learning episode and a larger drop in HRV during the learning interaction were associated with stronger behavioral performance on self-regulation and early academic skill assessments. Children's capacity to modulate their HRV in response to learning opportunities may be linked to their broader self-regulation and early academic skill development. Effects varied by episode and gender, underscoring a need for further research to rigorously evaluate the utility and generalizability of HRV in authentic educational settings.