Objective Surgical pulmonary vein isolation (PVI) for paroxysmal atrial fibrillation (PAF) blocks trigger stimulation from PVs and partially disconnects the atria from sympathetic and parasympathetic neural stimulation. This study describes long-term changes in heart rate variability (HRV) and autonomic activity (AA) after successful bipolar radiofrequency PVI. Methods Twenty-seven patients who underwent coronary artery bypass grafting and successful (defined as stable sinus rhythm for 1 year) off-pump bipolar radiofrequency PVI for PAF were prospectively followed 3, 6, and 12 months after surgery including 24 hours Holter electrocardiogram. The following HRV and AA parameters were calculated: mean NN-interval, SD of NN-intervals, SD of averaged NN-intervals, root mean square of successive differences, low frequency (LF) power (0.04–0.15 Hz; a parameter specific for sympathetic activity), high frequency (HF) power (0.15–0.4 Hz; a parameter specific for parasympathetic activity), and the LF:HF ratio. Results Preoperatively, high HRV and AA parameters were recorded. In 3-, 6-, and 12-month time, a progressive reduction of HRV and AA was observed, reaching significance after 12 months. Respective rates before surgery and 12 months after it were: for SD of averaged NN-intervals (122.4 ± 113; 80.5 ± 42 milliseconds; P = 0.046), for root mean square of successive differences (79.2 ± 93; 45 ± 20 milliseconds; P = 0.04). The LF:HF ratios were 1.22 and 0.73 before and 12 months after surgery, respectively. The statistically significant continuous reduction in LF:HF ratio (P = 0.02) is suggestive of a progressive parasympathetic dominance 12 months after surgery. Conclusions Successful PVI for PAF results in HRV and sympathetic activity reduction with preoperative sympathetic dominance and oncoming vagal dominance after 1 year from surgery. Despite preoperative sympathetic dominance, successful PVI for PAF results in HRV and a reduction in sympathetic activity with emerging parasympathetic dominance 12 months after surgery.