ECG screening can detect people at risk of developing atrial fibrillation (AF). Recent literature indicated that QRS transitional zone rotations could predict several cardiovascular events. Herein, we investigated the association between QRS transitional zone rotations and the future risk of AF. This prospective cohort study included 6794 participants (3178 men and 3616 women), aged 30–84 years, from the urban Japanese city of Suita. QRS transitional zone rotations were diagnosed by ECG during baseline, while AF was diagnosed by ECG, hospital records, and checkups during follow-up. The Cox regression was used to compute the sex-specified hazard ratios (HRs) and 95% confidence intervals (CIs) of incident AF for participants with counterclockwise and clockwise QRS transitional zone rotations compared to those with normal rotation. Within a median follow-up period of 14.6 years, 311 participants (206 men and 105 women) developed AF. Counterclockwise rotation was associated with the reduced risk of AF among men, but not women, in the age-adjusted model: HR (95% CI) = 0.66 (0.44, 0.98) and the multivariable-adjusted model: HR (95% CI) = 0.65 (0.43, 0.97). Clockwise rotation was not associated with AF risk in either sex. To the best of our knowledge, this is the first study to indicate that counterclockwise rotation could be associated with the reduced risk of AF in men. More studies are needed to confirm our findings and elucidate possible mechanisms.