Objective This study compared physiological differences between children diagnosed with migraine and their healthy peers. Method Physiological measures were obtained at baseline, after discussing an emotional stressor, and after a 5-min recovery period in 21 children with pediatric migraine and 32 healthy peers. Comparisons were also made on psychological measures investigating anxiety. Results Children with migraine exhibited a significantly higher pulse rate compared to comparison children at rest, and higher diastolic blood pressure and higher low-frequency/high-frequency ratio after a 5-min recovery from an emotional stressor. Additionally, when anxiety was entered as a covariate, group differences after the 5-min recovery period were no longer significant. Conclusions Results suggest that relative to comparison children, children with migraine exhibit some physiological elevation at rest, as well as a prolonged physiological recovery period after an emotional stressor. Group differences after the 5-min recovery period suggest that children with migraine experience delayed sympathetic hyperarousal and prolonged sympathovagal imbalance. The treatment implications of these findings are discussed