Ventricular arrhythmias (VAs) are common pediatric rhythm disorders requiring comprehensive laboratory evaluation. Although usually idiopathic, implying a benign character and favorable prognosis, the initial clinical approach is still not established in all cases. Considering their prognostic significance, exercise-induced (precipitated or aggravated) VAs usually require additional diagnostics, treatment, and follow-up. A number of reports have presented experimental and clinical evidence that increased sympathetic activity can initiate, or at least facilitate, VAs. Recent data highlight the relationship between exercise-induced idiopathic VAs (IVAs) and the long-term risk of cardiovascular death. The aim of this study was to assess the utility of heart rate variability (HRV) analysis as a noninvasive method for estimating autonomic nervous activity in children with exercise-induced IVAs. The study included 42 children with IVAs, who were divided into two groups: children with exercise-induced (precipitated or aggravated) IVAs and children with exercised-suppressed IVAs. Time-domain HRV parameters were analyzed from 24-h ambulatory electrocardiography recordings, and the majority of children underwent an exercise stress test using the McMaster protocol. The results of this study showed no significant changes in parasympathetic index, i.e., the square root of the mean of the sum of the squares of the differences between adjacent NN intervals (the length between two successive heartbeats) between the groups examined. On the other hand, we observed diminished time-domain values for the standard deviation of all adjacent NN intervals, as well as diminished time-domain values for standard deviation of the averages of NN intervals in all 5-min segments in the group of children with exercise-induced IVAs, implicating increased sympathetic activity in such individuals. HRV analysis could be a helpful diagnostic method, giving useful information regarding cardiac autonomic control in some children with exercise-induced IVAs.