Background Conventional right ventricular pacing (RVP) has been associated with an increased incidence of atrial fibrillation (AF). We sought to compare the occurrence of new‐onset AF and assessed AF disease progression during long‐term follow‐up between His bundle pacing (HBP) and RVP. Methods and Results We included patients undergoing initial dual‐chamber pacemaker implants at Rush University Medical Center between January 1, 2016, and June 30, 2019. A total of 360 patients were evaluated, and 225 patients (HBP, n=105; RVP, n=120) were included in the study. Among the 148 patients (HBP, n=72; RVP, n=76) with no history of AF, HBP demonstrated a lower risk of new‐onset AF (adjusted hazard ratio [HR], 0.53; 95% CI, 0.28–0.99; P =0.046) compared with traditional RVP. This benefit was observed with His or RVP burden exceeding 20% (HR, 0.29; 95% CI, 0.13–0.64; P =0.002), ≥40% (HR, 0.31; P =0.007), ≥60% (HR, 0.35; P =0.015), and ≥80% (HR, 0.40; P =0.038). There was no difference with His or RV pacing burden <20% (HR, 0.613; 95% CI, 0.213–1.864; P =0.404). In patients with a prior history of AF, there was no difference in AF progression ( P =0.715); however, in a subgroup of patients with a pacing burden ≥40%, HBP demonstrated a trend toward a lower risk of AF progression (HR, 0.19; 95% CI, 0.03–1.16; P =0.072). Conclusions HBP demonstrated a lower risk of new‐onset AF compared with RVP, which was primarily observed at a higher pacing burden.