BackgroundThe heart rate variability (HRV) is a non-invasive, objective and validated method for the assessment of autonomic nervous system. Although acute manifestations of COVID-19 were widely researched, long-term sequela of COVID-19 are still unknown. This study aimed to analyze autonomic function using HRV indices in the post-COVID period that may have a potential to enlighten symptoms of COVID long-haulers.MethodsThe 24-h ambulatory electrocardiography (ECG) recordings obtained >12 weeks after the diagnosis of COVID-19 were compared with age–gender-matched healthy controls. Patients who used drugs or had comorbidities that affect HRV and who were hospitalized with severe COVID-19 were excluded from the study.ResultsTime domain indices of HRV analysis (standard deviation of normal RR intervals in 24 h (SDNN 24 h) and root mean square of successive RR interval differences (RMSSD)) were significantly higher in post-COVID patients (p < 0.05 for all). Among frequency domain indices, high frequency and low frequency/high frequency ratio was significantly higher in post-COVID patients (p = 0.037 and p = 0.010, respectively). SDNN >60 ms [36 (60.0%) vs. 12 (36.4%), p = 0.028)] and RMSSD >40 ms [31 (51.7%) vs. 7 (21.2%), p = 0.003)] were more prevalent in post-COVID patients. Logistic regression models were created to evaluate parasympathetic overtone in terms of SDNN >60 ms and RMSSD >40 ms. After covariate adjustment, post-COVID patients were more likely to have SDNN >60 msn (OR: 2.4, 95% CI:1.2–12.8) and RMSSD >40 ms (OR: 2.5, 95% CI: 1.4–9.2).ConclusionThis study revealed parasympathetic overtone and increased HRV in patients with history of COVID-19. This may explain the unresolved orthostatic symptoms occurring in post-COVID period which may be associated with autonomic imbalance.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10840-022-01138-8.