Purpose Cather ablation is known to influence the autonomic nervous system. This study sought to investigate the association of sinus heart rate pre-/post-ablation and recurrences in patients with atrial fibrillation undergoing pulmonary vein isolation (PVI). Methods Between January 2012 and December 2017, data of 482 patients undergoing their first PVI were included. Sinus heart rate was recorded before (PRE), directly post-ablation (POST) and 3 months post-ablation (3 M). All patients were screened for atrial tachyarrhythmia recurrences during the one-year follow-up. Results In the total study cohort, the mean resting sinus heart rate at PRE mean 57.9 bpm (95% CI 57.1–58.7 bpm) increased by over 10 bpm to POST mean 69.4 bpm (95% CI 68.5–70.3 bpm); p  < 0.001 followed by a slight decrease at 3 M mean 67.3 bpm (95% CI 66.4–68.2 bpm) but still remaining higher compared to PRE ( p  < 0.001). This pattern was observed in patients with and without recurrences at POST and 3 M (both p  < 0.001 compared to PRE). However, at 3 M the mean sinus heart rate was significantly lower in patients with compared to patients without recurrences ( p  = 0.031). In this regard, patients with a heart rate change < 11 bpm (PRE to 3 M) or, as an alternative parameter, patients with a heart rate < 60 bpm at 3 M had a significantly higher risk of recurrences compared to the remaining patients (Hazard ratio (HR) 1.82 (95% CI 1.32–2.49), p  < 0.001 and HR 1.64 (95% CI 1.20–2.25), p  = 0.002, respectively). Conclusion Our study confirms the impact of PVI on cardiac autonomic function with a significant sinus heart rate increase post-ablation. Patients with a sinus heart rate change < 11 bpm (PRE to 3 M) are at higher risk for recurrences during one-year post-PVI.