Autonomic imbalance may play an important role in the pathogenesis of reversible cerebral vasoconstriction syndromes (RCVS). This study aimed to assess the autonomic function by analyzing heart rate variability (HRV) in patients with RCVS. Patients with RCVS and age- and gender-matched controls were consecutively recruited. All patients (both ictal and remission stage) and controls underwent 24-hour ambulatory electrocardiographic (ECG) recordings. HRV measures covering time and frequency domains were used to assess autonomic functioning. Thirty-nine patients with RCVS and 39 controls completed the study. Compared to the controls, RCVS patients during the ictal stage showed reductions in parasympathetic-related indices, including the root mean square of difference of consecutive interbeat intervals (RMSSD) (22.1 ± 7.0 vs. 35.2 ± 14.2, p < 0.001), the percentage of adjacent intervals that varied by more than 50 ms (pNN50) (3.7 ± 3.4 vs. 10.6 ± 8.1, p < 0.001), and high-frequency power (HF) (5.82 ± 0.73 vs. 6.77 ± 0.74; p < 0.001), and increased low-frequency/high-frequency (LF/HF) ratio (index of sympathovagal balance) (3.38 ± 1.32 vs. 2.48 ± 1.07; p =0.001). These HRV indices improved partially but remained significantly different from controls during remission. Decreased parasympathetic modulations and accentuated sympathetic activity might be a biological trait in patients with RCVS.