Beta-blockers are often used in the treatment of various heart diseases and affect the heart rate variability. In this study we aimed to assess the effect of various types of beta-blockers on the heart rate complexity in children using the multiscale entropy and detrended fluctuation analysis (DFA). The study involved 21 patients who were treated with beta-blockers for supraventricular tachycardia and 15 healthy children with normal cardiac assessments. The heart rate data was extracted from 24-hour Holter recordings and the DFA and multiscale entropy analyses were performed. The entropy was significantly higher in children who were treated with beta-blockers (MANOVA, p < 0.001). However DFA did not reveal significant difference between the two groups. Higher entropy indicates an increase in the heart rate complexity. Entropy and fractal behavior can change critically in disease states and the effect of beta-blockers can potentially be very useful in predicting clinical outcome.