Objective: Sample entropy (SampEn) gives an estimate of signal complexity in cardiac time series and can give information beyond linear heart rate variability. Lower cardiac SampEn is associated with psychopathology in adults. Emotional dysregulation is widely present in adult psychopathology and a forerunner to later mental problems in children. Therefore, this study investigated whether SampEn relates to emotional dysregulation in children. Methods: Participants were 32 children between 9 and 13 years with internalizing difficulties and 25 controls. Parents filled out the ‘Emotional Problems’ subscale in the Strengths and Difficulties questionnaire and the ‘Lability/Negativity’ scale in the Emotion Regulation Checklist. SampEn, root mean square of successive differences (RMSSD), normalized power of high frequency (HFnu) components of the cardiac signal and pre-ejection period (PEP) were computed at rest. The study investigated the predictive power of SampEn, RMSSD and HFnu on the measures of emotional dysregulation. It also tested whether RMSSD or PEP were related to SampEn. Results: SampEn was a significant predictor of both measures of emotional dysregulation, while RMSSD and HFnu were not. RMSSD and PEP were both significant predictors of SampEn. Conclusions: SampEn is a potential marker of dysregulation in the underlying neurovisceral processes vital for emotion regulation, and an important complementary measure to linear cardiac indices, explaining more of the variance in emotional dysregulation than RMSSD and HFnu in this study. Lower SampEn can also be linked to both higher vagal and sympathetic activation via RMSSD and PEP.