In search of more detailed explanations for body-mind interactions in physical activity, neural and physiological effects, especially regarding more strenuous sports activities, increasingly attract interest. Little is known about the underlying manifold (neuro-)physiological impacts induced by different motor learning approaches. The various influences on brain or cardiac function are usually studied separately and modeled linearly. Limitations of these models have recently led to a rapidly growing application of nonlinear models. This study aimed to investigate the acute effects of various sequences of rope skipping on irregularity of the electrocardiography (ECG) and electroencephalography (EEG) signals as well as their interaction and whether these depend on different levels of active movement noise, within the framework of differential learning theory. Thirty-two males were randomly and equally distributed to one of four rope skipping conditions with similar cardiovascular but varying coordinative demand. ECG and EEG were measured simultaneously at rest before and immediately after rope skipping for 25 mins. Signal irregularity of ECG and EEG was calculated via the multiscale fuzzy measure entropy (MSFME). Statistically significant ECG and EEG brain area specific changes in MSFME were found with different pace of occurrence depending on the level of active movement noise of the particular rope skipping condition. Interaction analysis of ECG and EEG MSFME specifically revealed an involvement of the frontal, central, and parietal lobe in the interplay with the heart. In addition, the number of interaction effects indicated an inverted U-shaped trend presenting the interaction level of ECG and EEG MSFME dependent on the level of active movement noise. In summary, conducting rope skipping with varying degrees of movement variation appears to affect the irregularity of cardiac and brain signals and their interaction during the recovery phase differently. These findings provide enough incentives to foster further constructive nonlinear research in exercise-recovery relationship and to reconsider the philosophy of classical endurance training.