While physical activity (PA) may influence resting heart rate (RHR), and a low RHR may be a risk factor for atrial fibrillation (AF), controversy exists regarding the association between PA and development of AF. Using data from a Korean, prospective population cohort, we investigated the independent effect of PA and RHR on the incidence of AF in the general population. A total of 8,811 participants aged 40-69 years were analyzed. Total PA assessed based on questionnaires was divided into quartiles, with the lowest to the highest being Q1, Q2, Q3, and Q4. During a median follow-up of 139 months, AF developed in 167 participants (1.9%). Q3 of total PA was associated with a significantly lower risk of AF than Q1 even after adjusting for RHR as a covariate, but Q4 was not. The risk of AF was higher in participants with RHR < 60 bpm than in those with RHR 70-85 bpm, and the significance persisted after adjusting for PA as a covariate. This study showed that a moderate amount of total PA was associated with a lower risk of incident AF independent of RHR and that low RHR was an independent risk factor for AF in the general Korean population.