Background: The modulation of the autonomic nervous system’s activity, particularly increasing its parasympathetic tone, is of significant interest in clinical physiotherapy due to its potential benefits for stress-related conditions and recovery processes. This study evaluated the effectiveness of the addition of neurodynamics in enhancing parasympathetic activation in subjects with chronic stress. Methods: A clinical trial randomly assigned participants to a group with neurodynamics (6 bpm breathing protocol + manual therapy + neurodynamic technique) or a group without neurodynamics (6 bpm breathing protocol + manual therapy only). Metrics of heart rate variability (HRV), including the Mean Heart Rate (Mean HR), standard deviation of intervals between consecutive heartbeats (SDNN), Heart Rate Difference (Diff. HR), Root Mean Square of Successive Differences (RMSSD), number of intervals differing by more than 50 ms (NN50), percentage of consecutive NN intervals that differed by more than 50 ms (pNN50), and the high-frequency component measured in standardized units (HF), were assessed before, during, and after the intervention. Results: During the intervention, the group with neurodynamics showed significant changes in all variables except in the pNN50 and HF while the group without neurodynamics only showed improvements in the Mean HR, SDNN, and RMSSD. In the post-intervention phase, the group with neurodynamics maintained an increase in HRV while the group without neurodynamics experienced a decrease, suggesting an increase in sympathetic activity. Conclusions: Vagal nerve neurodynamics appear to represent an effective method for enhancing parasympathetic activation in patients with chronic stress. The results highlight the importance of a more comprehensive analysis of HRV variables in order to obtain a correct picture of the impact of interventions on the complex and multifaceted functioning of the autonomic nervous system.