Vasovagal reactions may occur occasionally during electrical stimulation using interferential current (IFC). The purpose of this study was to examine variations in autonomic activity during the application of IFC in asymptomatic participants by analysis of their heart rate variability (HRV). Seventy-three male volunteers were randomly assigned to a placebo group (n = 36; HRV was documented for 10 min, both at rest and during a placebo intervention) and an intervention group (n = 37; HRV was documented for 10 min in two conditions labelled as (1) rest and (2) application of IFC technique on the lumbar segment). The diameters of the Poincare plot (SD1, SD2), stress score (SS), and the ratio between sympathetic and parasympathetic activity (S/PS) were measured. After interventions, differences amongst the placebo group and the IFC group were found in SD2 (p < 0.001), SS (p = 0.01) and S/PS ratio (p = 0.003). The IFC technique was associated with increased parasympathetic modulation, which could induce a vasovagal reaction. Monitorization of adverse reactions should be implemented during the application of IFC technique. HRV indicators might have a part in prevention of vasovagal reactions. Further studies in patients with lumbar pain are needed to explore possible differences in HRV responses due to the presence of chronic pain.