Vagus nerve stimulation (VNS) therapy has been recently incorporated in Latin America as a treatment for drug-resistant epilepsy. In particular, it is known that linear analysis and fractal parameters of heart rate variability (HRV) are able to indirectly measure cardiac autonomic activity. This case report presents a 17-year-old female with drug-resistant epilepsy implanted with a VNS device. In order to explore cardiac autonomic changes due to VNS, linear and fractal HRV indices were calculated in the presence and absence of neurostimulation. Novel fractal scaling exponents from HRV analysis were obtained from this patient and from a healthy control subject. Our results indicate that fractal indices of HRV, such as short-term scaling parameters from magnitude and sign analyses seem to be sensitive to the presence or absence of VNS, being confirmed by linear classical methods. This study shows that VNS therapy increases the complexity of cardiac fluctuations in a patient with drug-resistant epilepsy, reflecting an augmented HRV non-linearity and a diminished anticorrelated pattern in heart rate fluctuations. A potential clinical use of these parameters includes the early identification of bradycardia, sudden unexpected death (SUDEP) risk and preoperative VNS approaches. Thus, the scaling and magnitude properties of HRV have potential importance as a non-invasive and easy method for adequate diagnostic/prognostic implications in epilepsy treatment.