Background: Pathophysiology mechanism of primary focal hyperhidrosis (PFHH) is controversial. Heart rate variability (HRV) could explain if there is a systemic component present. We aimed to investigate the functions of the autonomic nervous system in patients diagnosed with PFHH compared to controls using the analysis of HRV in the domains of time, frequency, and nonlinearity, as well as analysis of the recurrence plots (RPs). Methods: We selected 34 patients with PFHH (29.4 ± 10.2 years) and 34 controls (29.2 ± 9.6 years) for HRV analysis. Heart beats were recorded with Polar RS800CX monitor (20 min, at rest, in supine position), and RR intervals were analyzed with Kubios Premium HRV software. RPs were constructed with Visual Recurrence Analysis software. Statistical analysis included unpaired t test (p < 0.05). Results: Our results showed that HRV parameters in the 3 domains evaluated did not show any differences between the groups. The same was observed with RPs. Conclusions: The findings suggest that PFHH, from the pathophysiological point of view, may be caused by peripheral involvement of the sympathetic nervous system (glandular level or nerve terminals), as there was no difference between the groups studied. More specific studies should help elucidate this issue.