Abstract Background Pulmonary vein isolation (PVI) using radiofrequency and cryoballoon ablation (CBA) modulates the cardiac autonomic nervous system (ANS) by affecting epicardial ganglionated plexi. In contrast, pulsed field ablation (PFA) appears to exert minimal autonomic effects. The impact of cardiac ANS modulation on arrhythmia recurrence remains incompletely understood. Methods In this multicenter trial substudy, 210 patients with symptomatic paroxysmal atrial fibrillation (AF) were randomized 1:1 to PVI using PFA or CBA. All patients received an implantable cardiac monitor at the time of ablation. Daytime heart rate (DHR), nighttime heart rate (NHR), and heart rate variability (HRV) were continuously recorded over 12 months and analyzed at day 1–2, month 3, 6, 9, and 12 post-ablation, and related to arrhythmia-free outcome. Results PFA (n = 105) was associated with higher HRV at day 1–2 compared to CBA (n = 105; 100 [79–122] ms vs. 73 [59–93] ms, p < 0.001). This trend persisted throughout follow-up. DHR and NHR were also consistently lower in the PFA group. Freedom from arrhythmia recurrence at 12 months was higher with PFA than CBA (63% vs. 49%, p = 0.046). HRV did not differ between PFA patients with and without recurrence. A stronger initial HRV suppression predicted favorable outcomes in CBA patients (67 ms vs. 84 ms in patients without vs. with arrhythmia recurrence, p = 0.002). Conclusions Despite reduced cardiac ANS modulation, PFA was associated with a superior arrhythmia-free outcome compared to CBA. These findings suggest that cardiac ANS modulation may not be critical for the successful ablation of paroxysmal AF.