Background: New-onset atrial fibrillation (NOAF) is associated with adverse outcomes in patients with coronary artery disease (CAD). Although newer generation drug-eluting stents (NG-DESs) are more beneficial than bare-metal stents (BMSs) in reducing the risk of in-stent restenosis and revascularization, whether NG-DES implantation in patients with stable CAD reduces NOAF risk compared with BMS implantation remains unknown. Methods: This population-based cohort study was conducted using data from Taiwan's National Health Insurance Research Database. Propensity score matching was used to select 18,423 pairs of patients with stable CAD receiving NG-DES implantation and BMS implantation with similar baseline characteristics for evaluation. A competing risk model was used to evaluate the risk of NOAF between the NG-DES and BMS groups in which death was considered a competing risk. Results: After adjustment for patients' clinical variables, the use of NG-DESs was associated with a decreased risk of NOAF at 1-year follow-up (adjusted subdistribution hazard ratio [SHR] = 0.79, 95% confidence interval [CI] = 0.68–0.93, P = 0.005) compared with the use of BMSs. Similar results indicated that NG-DESs were beneficial for reducing the risk of NOAF (adjusted SHR = 0.81, 95% CI = 0.67–0.97, P = 0.020) in patients with a CHA2DS2-VASc score of ≥2. These findings were also consistent with those for patients who received dual antiplatelet therapy for an undefined duration of >1 month following stent implantation. Conclusions: Our findings suggest that NG-DESs might reduce the risk of NOAF in patients with stable CAD.