Background: Primary focal hyperhidrosis (PFH) is associated with autonomic nervous activity, and studies investigating this association in patients with PFH are very important. Heart rate variability (HRV) is a simple and noninvasive electrocardiographic test showing activity and balance in the autonomic nervous system, which consists of sympathetic and parasympathetic components. The aims of this study are to investigate associations between autonomic nervous activity and hyperhidrosis characteristics using HRV and to investigate the association between HRV findings and compensatory hyperhidrosis (CH) after sympathectomy. Methods: From March 2017 to March 2020, 105 subjects with PFH who underwent preoperative HRV tests and sympathectomy were analyzed. All subjects underwent bilateral thoracoscopic sympathectomy. T2 sympathectomy was conducted for craniofacial hyperhidrosis, and T3 sympathectomy was conducted for palmar hyperhidrosis. The following HRV parameters chosen to investigate the association between hyperhidrosis and autonomic nervous activity were measured by time and frequency domain spectral analysis: (I) time domain: standard deviation of normal-to-normal interval (SDNN) and square root of mean squared differences of successive normal-to-normal intervals (RMSSD), (II) frequency domain: total power (TP) of power spectral density, very low frequency (VLF), low frequency (LF), and high frequency (HF). HRV parameters were analyzed according to hyperhidrosis type (craniofacial vs. palmar type), sweat reduction, and CH after sympathectomy. In addition, the independent HRV parameters influencing CH after sympathectomy were investigated with multivariate analysis. Results: Craniofacial hyperhidrosis was significantly more prevalent in the old age group (P<0.001).Sweat reduction after sympathectomy was significantly more prominent in palmar hyperhidrosis (P=0.037), and CH after sympathectomy was more prominent in craniofacial hyperhidrosis (P<0.001). Palmar type patients exhibited significantly larger SDNN, RMSSD, TP, LF, and HF than craniofacial type patients (all P<0.001). There were no significant differences in any HRV parameters according to sweat reduction after sympathectomy. Low-degree CH was associated with significantly larger SDNN, RMSSD, TP, LF, and HF than high-degree CH (P<0.001, P<0.001, P=0.002, P=0.001, and P<0.001, respectively). Multivariate analysis showed that HF and age group were associated with CH after sympathectomy (P=0.007 and P=0.010, respectively). Conclusions: This study shows that HRV can provide useful insight into the pathophysiology of PFH and enhance preoperative risk stratification of CH. Large-scale, prospective studies are required to determine the predictive value of HRV in patients at risk for subsequent CH after sympathectomy.