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Background: Stroke survivors often experience autonomic nervous system (ANS) dysfunction. While Transcranial Direct Current Stimulation (tDCS) has been shown to modulate the ANS when applied to the left hemisphere, its effects on the right hemisphere remain unexplored. Objective: We aimed to compare the effects of tDCS applied to both the injured and the contralateral hemispheres on heart rate variability (HRV) and functional capacity in individuals post-stroke. Methods: Twenty individuals with cerebral hemisphere lesions (ten with right-hemisphere lesions and ten with left-hemisphere lesions) were randomized into four groups: anodal and sham tDCS on the left temporal cortex (T3) and anodal and sham tDCS on the right temporal cortex (T4). HRV was assessed before the intervention, after the six-minute walk test (6MWT), and following tDCS. HRV data were categorized into frequency ranges: low frequency (LF), high frequency (HF), and sympathovagal balance. The 6MWT (meters) was conducted both pre- and post-tDCS. Results: In individuals with right-hemisphere lesions, a higher global LF value was observed (right side: 71.4 ± 16.8 nu vs. left side: 65.7 ± 17.3 nu; p = 0.008), as well as lower values of the HF component (right side: 29.5 ± 18.9 nu vs. left side: 34.0 ± 17.4 nu; p = 0.047), consequently exhibiting higher global values of the low/high-frequency ratio (right side: 3.9 ± 2.8 vs. left side: 2.9 ± 2.4). Regarding the stimulation site, tDCS over T3 led to a lower overall value of the low/high-frequency ratio (left hemisphere: 3.0 ± 2.2 vs. right hemisphere: 3.7 ± 2.9; p = 0.040) regardless of the lesion location. A significant increase in the distance covered in the 6MWT was observed for individuals with lesions in both hemispheres after tDCS at T3. Conclusions: Participants with right-hemisphere lesions exhibited superior global sympathetic autonomic nervous system activity. When the tDCS was applied on the left hemisphere, it maintained lower sympathovagal balance values and improved functional capacity regardless of the hemisphere affected by the stroke.