The aim of this study was to assess the heart rate variability (HRV) at rest and during active orthostatic challenge in long COVID patients with orthostatic intolerance symptoms (dizziness, pre-syncope, and syncope). We performed a cross-sectional, observational, comparative study of 60 subjects of both sexes, aged 18 to 60 years (31 met the criteria of long COVID, 15 were infected individuals without symptoms, and 14 who had neither infection nor symptoms formed the age-matched control group). HRV was obtained from continuous electrocardiograms in a supine position and active standing with spontaneous breathing. The time from SARS-CoV-2 infection to testing in the COVID-19 group was 573 ± 289 days. The resting (supine position) values of SDNN, RMSSD, SD1, and SD2 were lower in long COVID patients than in control participants, while all other HRV indexes were similar between groups. In response to active standing, both groups had similar changes in all HRV indices. In conclusion, an active orthostatic test was not able to exhibit an autonomic dysregulation in these patients with long COVID, suggesting that cardiac autonomic modulation may have recovered due to the long time that elapsed after SARS-CoV-2 infection.