Background: An association has been demonstrated between heart rate variability (HRV) and cardiac events in some diseases. However, the association with new-onset atrial fibrillation (AF) after coronary artery bypass graft (CABG) is still controversial. This study aimed to investigate the association between HRV and new-onset AF in patients undergoing CABG during a 6-month follow-up. Methods: This cross-sectional study involved 119 consecutive patients undergoing off-pump CABG. All patients were assessed with 24-hour Holter recordings 2 days before CABG and 1 week, 3 months, and 6 months postoperatively. HRV was analyzed, and AF was detected from its recordings. Main results: In patients undergoing CABG, NYHA III increased the AF rate at 7 days, and advanced age and diabetes were associated with AF at 6 months postoperatively. A reduction in time-domain measurements before surgery was significantly associated with a higher risk of developing AF at 7 days postoperatively, no association between preoperative HRV and AF was found at 6 months. Reduced preoperative HRV (SDNN < 50 ms) was the independent predictor of AF at 3 months (AUC = 0.65) and 6 months (AUC = 0.62) following surgery. Conclusions: A reduction in time domain before CABG was associated with a higher risk of new-onset AF at 7 days postoperatively but not at 6 months. SDNN <50 ms was an independent predictor of higher incidence of AF at 3 and 6 months post surgery.